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Begonia Stem Rot — Identification, Treatment, Prevention

Begonia Stem Rot —  Identification, Treatment, Prevention

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Beautiful begonias are loved the world over for their colorful varieties. Popular as both a houseplant or as a plant in a raised bed, they come in a range of sizes and colors. 

Generally pretty easy to care for, they usually like moist but well-draining soil and need to be protected from frost. 

So popular are begonias that we feature extensive coverage and care guides on this website. In this guide however, we will focus on the prevention of a condition known as begonia stem rot. 


Begonia Stem Rot

Caused by the Pythium ultimum bacteria that becomes activated in wet soil conditions, begonia stem rot is usually fatal to the plant. Keep the risk to your plants low by ensuring your soil is well-draining and that you do not overwater.

Make sure you do not accidentally spread the spores around to other plants by moving soil around or using contaminated tools.


What exactly is begonia stem rot?

Begonia stem rot is a pretty serious condition that can be fatal for an otherwise healthy begonia plant. It is often also known as begonia pythium rot due to the causal agent – the pythium ultimum fungi. 

Thriving in damp environments, the fungi spread easily, and can even be transferred to other parts or areas of your garden in order to strike on another plant later. 


What does begonia stem rot look like?

The typical signs of pythium or begonia stem rot are usually a blackened stem. The plant will likely begin to slow right down in terms of growth, and the stems become clogged with water. 

Your begonia will probably start to droop too, and to your shock you may see whole stems simply falling over. 

In a severe case you may be checking the leaves gently and find the stem just falls completely away. On further inspection, you will likely see that the stem has rotten away. 

Finally, you may notice that the soil remains constantly wet and doesn’t drain as fast. This is a sure sign that the root system of the plant is saturated and unable to absorb any water – and therefore any nutrients. 


What triggers begonia stem rot?

We know that begonia stem rot is caused by the pythium ultimum fungi. But what we need to work out is just what conditions trigger the fungi to becoming active and start to attack the plant.

Well, the key factor here is a damp environment. The fungal spores can lie dormant from season to season, and are activated in wet soil. 

Once this happens it is very hard to control, especially as the infection can recur annually in different areas of your garden depending on whether you moved the soil. 


Be careful – begonia stem rot can spread easily 

If you spot the signs of this infection you have a couple of problems. First, you will have to deal with the infected plant (more about that shortly). 

But you also need to take special care that you do not spread any of the spores around the rest of your plants and garden. 

Firstly, make sure to not cross-contaminate the area by not reusing the soil anywhere else, or spreading it over a wider area. 

Secondly, any tools you use on the affected begonia will need to be sterilized before you use them again. You may also find it useful to sterilize or destroy any of the pots in which the infected plant was kept. 


How to treat a begonia with stem rot

Stem rot is a serious condition, and is usually fatal to the plant. Whilst other conditions such as root rot can sometimes be stopped if caught early enough, it is usually best to start over with a new plant in the case of a pythium ultimum infection. 

That is because it really does spread so easily to other, healthier plants. Destroy the plant, sterilize the soil and remove the pots. 

It is best to eliminate all evidence of the infection, but if you have really nice pots you may want to keep them. In that case, you should steam clean the pots at consistently hot temperature in order to kill any remaining fungal spores. 


Top tips for preventing stem rot in begonias

Since your begonia can rarely be saved once a stem rot infection has taken hold, your best chance is to make sure it never happens in the first place. 

Here are some tips you can follow in order to reduce the likelihood of begonia stem rot happening to your plants. 


Avoid overwatering

Too much moisture in the soil is the number one cause of stem rot. Whilst this plant likes moist soil, pooled water is a no-no.

Make sure that water drains through the soil quickly, and if you notice it is sitting for too long around the base of the plant you need to drill more drainage holes or mix better draining soil.

Water around once a week in the growing season and only when the top layer has dried out. 

In the dormancy period, ease off the watering and only do it once a month or so.  Another tip – don’t let the plant sit in a plate of water if you are heading on vacation. 


Ensure you use well-draining soil

One of the key factors in helping to avoid begonia stem rot is to ensure your soil drains thoroughly between waterings. This is especially true in cooler temperatures. Make sure your soil is well-draining by mixing perlite in to the pot or soil. 


Heat up the soil

Another trick to cover the soil in plastic for several weeks before planting. As temperatures rise the soil will heat up, which in turn should kill out any fungal spores buried in it. 


Do not reuse old soil

If you have had a previous infection it is key that you either sterilize the soil completely, or start from scratch with a new fresh batch.

The same can be said too for the pots, as well as any tools. Be careful not to move soil around your garden or into other pots to eliminate any risk of cross-contamination. 


Try a fungicide

Fungicides can be used in the control of stem rot. On a dry day, put some mefenoxam fungicide on to the soil. These can usually be bought in a powder form that can be directly applied to the area and then activated by watering. 


Frequently asked questions about begonia stem rot


What causes begonia stem rot?

Moist and damp soil conditions coupled with the presence of the Pythium ultimum fungi cause this infection. Spores lie dormant in the soil and are activated when conditions are just right – damp and warm soil environments being the main trigger. 


Can I save my begonia once stem rot has set in?

If caught very early it may be possible to cut out the affected portion and treat with a fungicide. However, as the infection is fairly aggressive it is usually better to destroy the plant and any pots and soil it was in, and start from scratch. 



Begonia stem rot is a particularly dangerous condition that is usually fatal to the plant. As it is usually hard to recover from, the best method for treatment is actually the prevention of the condition in the first place.

If you stick to the tips in this guide you will be well on your way to saving your begonias from this nasty condition before it can take hold!