starting bonsai from seed

Starting a Bonsai From Seed

Introduction: Starting a Bonsai From Seed

Most Bonsai take years to train before you can call them finished so this is not the hobby for an impatient person. The only good part is other than watering you only touch them about once every couple months so they can recover from pruning. Trees and shrubs that need to winter can go for four to six months when you winter them. This gives you time for other things in your life.

Larger Bonsai can be trained from nursery stalk, but smaller Bonsai one hand or less can be easier to train from seedlings and seed stalk.

I had 10 one handed Bonsai, (5 to 8 inches tall) at one time. Most were North American trees that I started as seeds or seedlings. My oldest Bonsai was a Japanese White Pine I had been training for 10 years.

I went through a great deal of work getting an Oak, a Maple, and a Willow, started when I lost all my Bonsai. Our goat got into where I was wintering my Bonsai and ate all of them to the point every tree died. So keep your pets and other animals away from your Bonsai, or kiss your Bonsai good bye. For this reason I grow my Bonsai indoors.

Step 1: Tree Selection

Although I have raised broad leaved Bonsai, pine trees, juniper, and other conifers, with small foliage make great Bonsai that remain green year round. For this Instructable I am going to raise a White Spruce pine Bonsai from seed. Its small needles and cones make it ideal for a midsize or larger Bonsai, (10 inches and up). I am going to try to keep it less than 10 inches.

This 2 year old 2 inch tall seedling shows the beginning of a White Spruce’s development. The first year’s growth is a single stem, and at the end of the first years growth sprouts the second years growth usually 3 stems.

Since Bonsai take years I will show pruning a four year old Cedar in the last step.

Step 2: Seed Collection

Find a tree you like, look for a tree that has the traits you want in your Bonsai, and gather mature cones from the tree, they should be brown but not fully open. Green cones are immature and the seeds may not be fully developed, and open cones can lose their seeds to falling out and birds.

Other than rain forests, many conifers have a symbiotic relationship with fire and the white Spruce is no different. Spruce trees like many other pine trees, needs a forest fire to spread their seeds most of the time.

They start to produce cones when they are quite tall, 15 to 20 feet tall, the cone starts off small and green in the spring and grow during the summer turning brown in the fall. The mature cones look much like the skin of an Armadillo. The cones protect the seeds from birds and stay on the tree for a couple years until they open and fall off the tree or a forest fire opens them.

In a forest fire the heat from the fire causes the cone to open and after the fire passes the seeds fall to the ground replanting the forest to grow until the next forest fire. I am going to use the same process to harvest my seeds.

Place the cones in a dish and bake them in the oven at 350⁰, this will open the cones so you can just tap the cones hard to make the seeds fall out.

Step 3: Separating the Seeds

Since the spruce cones are only the size of a peanut, instead of tapping them on a hard surface I placed a hand full of open cones in a jar, and shook the jar until I could see the seeds collecting on the bottom of the jar.

Then I dumped the contents of the jar in a bowl and separated the cones from the seeds.

I repeated this process until I had all the seeds from the cones, don’t worry if you have what might appear to be too many seeds. Not all the seeds will germinate when you plant them and some of the seedlings will just plane fail. You can clean off the chaff and drop the seeds in water then plant only the seeds that sink, but unless you want to improve your chances of cluster seedlings it is not necessary. (Cluster Seedlings are seedlings growing close together.)

Step 4: Nursery Planting

In a nursery they place the seeds in starter trays, once the trees sprout they are transplanted to a growing field, and once they are ready for market they are transplanted to pots for sale.

When planted this way the taproot grows down and the secondary roots grow out from the taproot supplying the tree with nourishment. In a young tree the taproot can be as long as the tree is tall. This makes working with wild or nursery stalk challenging because to make these trees into a Bonsai you need to cut back the taproot.

Cutting back the taproot takes time, if you take too much of the taproot you kill the tree because you won’t have enough secondary roots supplying the tree with nourishment.

Start by cutting no more than a third of the taproot and pruning back a third to half of the foliage, with less foliage the roots don’t need to supply as much nourishment, and let the tree grow and recover from pruning.

Repeat this process as many times as necessary until your root bundle is the size you need for your finish pot, then train the top of your tree if need be.

Step 5: Shallow Planting the Seeds

I start with a shallow tray and place the seeds on the bottom of the tray, and then I put an inch of topsoil on top of the seeds and water. This causes the taproot to grow horizontally and the stalk or trunk of the seedling to grow upwards.

This type of planting is training your Bonsai from germination and you don’t have to cut back the taproot as drastically. Almost the entire root cutting is the ends of the secondary root tips and you are able to plant the tree in a shallow dish right from the start of training. You are able to train the trees top in its first year if you want, and you can make the smallest of Bonsai, Poppy-Seed Bonsai. (Bonsai 1 to 3 inches tall.)

Step 6: Pruning a Three Year Old Cedar

I started these cedars four years ago, the two of them were close enough they looked like one tree. I am going to lock them together so that in time they will grow into one tree giving me a tree trunk that looks twisted.

The tools I will be using are grooming tools, a pair of side cutting nail trimers, a long tweezers, and a pair of nail scissors.

After removing the unwanted foliage you can clearly see the two trunks and the horizontal taproots.

Last using the remaining foliage I locked the two trunks together so that in time they would become one.

Starting a Bonsai From Seed: Most Bonsai take years to train before you can call them finished so this is not the hobby for an impatient person. The only good part is other than watering you only touch them about once every couple months so they can recover from pruning. Trees …

Growing a Bonsai From a Seed

Now a world wide phenomena, the Japanese art of bonsai can provide hours of enjoyment and relaxation. If like many artists you wish to be in charge of your creation from the early stages it is possible to grow your own bonsai tree from a seed. There are also other options in the early stages such as growing from a seedling, sapling or even cloning your favorite tree.

Growing a Bonsai From a Seed

Known as Misho in Japanese, growing a bonsai from a seed is an extremely rewarding venture. It is, however, one which takes great patience. Choosing to grow your bonsai tree from a seed can be a positive experience for a number of reasons. First and foremost, you have absolute control from the very beginning stages, you can train your bonsai as it grows and thus there is no need to re train. It is also cost effective and with a little research can be relatively easy. Fully your own creation, the satisfaction when it finally grows is unsurpassed.

The drawback is that you will have to wait around three years before being able to shape or style your bonsai tree. If you’re a beginner keen to get started in the art of bonsai, you might want to plant a bonsai from a seed but simultaneously buy an established bonsai that you can begin to work and learn on immediately.

Which Species Of Seeds Should You Start With?

There are hundreds of species of tree which make beautiful bonsai including Elms, Maples, Junipers, cedars and Pines. You should pick the species of bonsai tree you would like to grow in accordance with your environment and experience. If you are looking to grow an indoor bonsai you will want to look at tropical/subtropical species. If you are growing your bonsai outdoors research which trees are indigenous to your area. Choosing seeds which are indigenous is a wise choice.

If you are a beginner, you will want to opt for a species which is more forgiving to beginner mistakes.

Where To Get Your Seeds

If you have decided that Misho is for you then you will need to start by obtaining seeds. Bonsai is the ancient Japanese art of training and pruning a tree which is contained by planting it in a container and therefore, there is no such thing as a special seed for a bonsai tree. You simply need seeds from a normal tree to begin the process. There are two ways to obtain seeds. The first is to collect them locally, this is the easiest route for beginners. The best time to collect seeds is late summer or early autumn.

Collecting Seeds

If you want to grow a coniferous bonsai, collect the cones from the tree, making sure they are brown and closed, green cones have not matured and open cones will most likely have lost their seeds already. Take the pine cones home, spread them out on a tray and keep them in a dry, warm place. The pine cones should dry out and open, allowing the seeds to be released. If you have any difficulty in removing the seeds you can use tweezers to gently tease them out.

Buying Seeds

The alternative to collecting your own seeds would be to purchase them from a garden center or order them online. Research which type of seeds you wish to purchase and buy from a reputable seller. There are also bonsai growing kits that you can purchase to get you started.

This one is superb for beginners and comes with everything you need:

How to Plant Seeds for a Bonsai Tree

If you have collected your seeds locally, it should be fine to go ahead and plant them in late autumn, allowing them to follow their natural cycle. They should be in tune with the climate and present little problem germinating.

If you have purchased seeds which are unaccustomed to the climate or you wish to plant out with planting season, the seeds will require pre treatment You will need to complete the process of scarification and/or stratification before you begin planting. Check the instructions on the packaging of your seeds.

To avoid stratification, the preferred option for a beginner would be to collect seeds locally.


Scarification is the process of weakening the hard shell of a seed to speed up germination. Some seeds will benefit from scarification before stratification. Scarification can be done to seeds before stratification and also to seeds that have hard, tough shell and are stubborn and difficult to germinate such as the Redbud (Cercis canadensis) and the eucalyptus.

There is more than one method of scarification

Method 1 – Using sandpaper or a nail file rub the seed all over until it is noticeably dulled.

Method 2 – Using nail clippers or a knife put a definite but small nick in the seed.

Method 3 – Place the seeds in a small container of hot but not boiling water, a temperature of around 80 degrees is perfect. Leave them in the water as it cools, soaking for 12 to 24 hours. This helps to soften the seeds coat considerably. Seeds which float to the top should be discarded.


Stratification is the simulation of the natural conditions which seeds require before they will germinate. Many species of tree have a winter dormancy phase; the seed will not be ready to grow until this dormancy is broken.

Cold Stratification Steps

  • Step 1: Soak your seeds in water.
  • Step 2: Fill a plastic bag (a zip lock food bag is perfect) with moist potting soil, many bonsai enthusiasts recommend peat moss or sand. It is important to note here that the substrate should be moist but not soaked.
  • Step 3: Place the tree seeds in the bag and seal.
  • Step 4: Place in the fridge at a temperature below 10 degrees.

It is important to keep a check on your seeds, watching carefully for any signs of fungus. A fungicide can be mixed into the bag with the seeds and soil if required. The period of stratification required can differ greatly between species. They will usually need somewhere between 21 and 90 days. When the seeds sprout they are ready to be removed from the fridge and planted.

Planting Your Bonsai Seeds

Now that your bonsai seeds are ready, lets go through the planting process step by step:

Step 1: Using a 5inch pot, spread a layer of your chosen substrate. This should be a coarse water draining substrate
Step 2: Add your chosen bonsai soil. Choosing the correct soil is important for a healthy bonsai. Check out our soil guide for more advice and information.
Step 3: Spread the seeds evenly across the soil, making sure to leave space between them.
Step 4: Cover the seeds with a top layer of soil and gently compact with your fingers.For the top layer of soil 2 – 3cms will be ample.
Step 5: Water well.

Around 6 weeks after your bonsai sprouts you can begin to use small amounts of fertilizer.

Bonsai Seedlings

When your bonsai has grown from a seed to a seedling you will need to transfer it into it’s own little individual pot, but you must take great care not to damage it. It’s is extremely delicate at this stage, whilst transferring ensure the roots do not dry out. Left to grow as a normal tree, the seedling develops a tap root, this is the root which will anchor down into the ground and spread through the soil to look for the essential nutrients. With bonsai this root should be removed preferably within the first year, the lateral roots should then be diverged out evenly to become the nebari (surface roots).

Planting/Transferring Your Seedling Step by Step

  • Step 1: Gently remove your seedling from its current tray or pot. Try to push it out gently from underneath.
  • Step 2: Spray the roots so they are clean and wet. Do not let them dry out during the process.
  • Step 3: Identify the tap root.
  • Step 4: Carefully remove the tap root with sharp scissors.
  • Step 5: It is useful to spray a little root hormone on the remaining roots to encourage growth.
  • Step 6: Using a chopstick or bamboo create a small hole in your chosen substrate.
  • Step 7: With care and caution place the root mass into the hole.
  • Step 8: When you are happy with the position use your finger to work the soil back into the gap until your seedling is secure.

Growing a Bonsai From a Sapling

A sapling is a young tree between the approximate ages of 1 to 3 years. Saplings are a great way to start off growing your bonsai tree. There is no need to pick a dwarf tree to begin with, excellent bonsais can be made from a large variety of normal young trees. Pick a species which is suitable for bonsai. It must be able to withstand being in a container and having it’s roots and branches heavily pruned.

Aesthetically you should look for a sapling which is wider at the bottom and gets thinner as the trunk goes up. The lower branches should be shorter whilst the branches at the top should be longer. Desirable qualities for bonsai are smaller leaves or needles and an attractive bark. Proportion is important in the creation of a bonsai so look for a sapling which is proportionate. Saplings are easy to train if you carefully prune and confine both the roots and tree canopies.

When picking your sapling look for a tree that is young and healthy. Gently release the tree from the ground or pot where it is currently growing. Clean the roots, rinsing gently until they hang downwards from the tree. If the tap root has not been removed do so following the same steps as above for a seedling. There are some species such as oak trees that after a year or two of growing in the ground will not do well having their tap root removed.

Prune the tree in a way that is suggestive of the bonsai form you hope to create in the future. A sapling around 1 or 2 years old will have a trunk which can still be easily manipulated, you can change its form by placing the pot at unusual angles and changing the position annually or with gentle wiring.

The form of your bonsai is not determined solely by either training or species but by a combination of both as such it is something to consider when choosing a sapling. Some species are more adept to certain forms and will prove easier to train.

Check our Bonsai Wiring Guide for more tips on how to train your bonsai tree!

Now a world wide phenomena, the Japanese art of bonsai can provide hours of enjoyment and relaxation. If like many artists you wish to be… ]]>