Geranium Stem Rot: What Is It And How To Control Rotting Stems

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The topic of geraniums can be a confusing one for many people.

Many of the plants you think of as geraniums aren’t geraniums at all but plants that were formerly a namesake genus.

geranium stem rotPin

In the case of geraniums, true geraniums are often called “hardy geraniums” due to their higher resilience.

All other geraniums are Pelargonium (pe-lar-GO-nee-um), roughly half the size of the Geranium (jer-AY-nee-um) genus. They make up the vast majority of geraniums grown and sold.

All geraniums are susceptible to rot. On older plants, the rot may start underground in the roots, but the result is the same. Overwatering can exacerbate the problem, and it can be spread by fungus gnats.  

Pretty much every gardener knows about root rot, but did you know that stem rot is also a significant risk often caused by the same fungi?

Here’s everything you need to know to combat stem rot in both geraniums and pelargoniums.

What Is Stem Rot?

Stem rot is a condition that many fungal infections may cause.

Some, such as Pythium spp., may cause both leads to root rot and stem rot. In the case of pythium, the stem rot is called blackleg.

Stem rot is usually caused by overwatering. But it could also be due to cross-contamination or infected soil.

Infection was obtained on Coleus cuttings, which were rapidly discolored and subjected to a shriveling dry rot without any stoppage of infection, as in the case of geranium cuttings.

While the symptoms are a bit different from root rot, it’s every bit as deadly and often more brutal to treat once the infection sets in.

What Damage Does Stem Rot Cause?

Many of the symptoms of stem rot may come from other conditions.

The leaves will often turn yellow or brown and will begin to wilt.

Meanwhile, the stems will brown and then blacken as the infection spreads.

For the most part, there’s no cure for stem rot. But plants can often still be salvaged if the decay is caught in time.

Because the fungi that cause stem rot – often referred to as water molds – can survive for long periods in the soil level, cross-contamination can be a risk.

Since these fungi attack most plants, the risk of stem rot spreading to nearby plants is also high.

Early action is the best chance to save your geranium. Move healthy geraniums in the same pot or same area of the garden because the bacteria and fungus can continue to live in the soil even after removing the problem plant. 

Geranium Plants Diseases 

The primary diseases encountered on seedling geraniums are Damping-Off, Pythium Root Rot, Rhizoctonia Root and Crown Rot, and Botrytis Blight, Crown Rot, and Flower Blight. 

Generally, leaves of geranium affected with bacterial blight will be spotted, the roots will remain white and healthy, and vascular discoloration will be less pronounced or absent (see a comparison of bacterial blight and Southern wilt symptoms on geranium ).

Alternaria spots tend to be larger in size; additionally, under conditions of high humidity, dark-brown, fuzzy spore masses of the fungus cover the Alternaria spots.  

Highly developed plants have two types of vascular tissues: the xylem and the phloem vascular bundles, and particularly in the xylem, it is responsible for the transportation of raw sap (water and nutrients) from roots to aerial parts of the plant.  

The common geranium (Pelargonium hortorum) is susceptible to this disease. No geranium cultivars are resistant. 

Symptoms The initial symptoms include a wilting of the lower leaves followed by chlorosis and, finally necrosis of the leaves. 

If you examine the lower surface of the leaves and notice raised quarter- to half-inch water-soaked spots, it’s time to suspect Alternaria leaf spot. Caused by the fungus Alternaria alternata, it usually starts on the lower leaves before moving up to the higher ones.  

Three bacterial diseases are known to attack geraniums: bacterial blight or wilt, southern bacterial wilt, and bacterial leaf spot. Bacterial blight or wilt is the only one of these diseases currently known to occur in the Midwest.  

This disease is caused by the bacteria Xanthomonas campestris pv. pelargonii. Once the plant is impacted, there is no cure. 

To avoid it, wash your garden tools, water at the soil level, and purchase plants that look healthy and show no signs of disease.  

In Wisconsin, commercial and home gardeners have lost many plants to bacterial stem rot and leaf spot. This disease produces three distinct types of symptoms: stem rot and leaf wilt, leaf spot, and general unhealthiness of the plant.  

  1. Botrytis blight, caused by the fungus Botrytis cinerea, impacts the flowers first – which is both good and bad news. It’s good because this means you can usually spot it and start treating your plants quickly.  
  2. Rust is a common disease that impacts many different plants, but the fungus that specifically attacks geraniums is Puccinia pelargonii-zonalis.
  3. If you imagined that a disease with “wilt” in the name would result in wilting leaves, you’d be right. Verticillium wilt can look a lot like bacterial blight because the plant simply turns brown and collapses.   

How To Control Stem Rot?

As mentioned, there’s no actual cure for stem rot once it sets in, but you can control it if caught early on.

Examine the stems of the infected plant. 

Symptoms are most likely to occur during periods of warm weather and when plants have been on a high-nitrogen fertilizer program and are growing luxuri- antly. Stem rot and leaf wilt are the most conspicuous symptoms.  

Stems that are still primarily green may often be pruned down or treated. But severely blackened limbs must be destroyed.

A severely infected plant needs discarding.

There are three methods of combating stem rot: chemical fungicides, neem oil, and repotting.

Chemical Fungicides

For chemical fungicides, choose a product marked for stem rot and apply as directed.

Allow the soil to dry out, or the rot will return.

It’s best to temporarily uproot the plant, treat it, and sterilize the soil before replanting.

Note that fungicides will not be able to restore severely damaged stems.

Neem Oil

Perhaps the gardener’s best friend, raw neem oil in the form of a soil soak, can help fight off root rot and stem rot. But it won’t restore severely damaged stems.

The soil soaks work by being absorbed into the roots. Neem’s principal active ingredient, Azadirachtin, becomes a systemic pesticide that helps protect the plant for up to 22 days.

While not strictly a fungicide, neem oil can help combat many fungi and bacteria.

Once again, you will need to let the soil dry out for any treatments to be effective.

The neem oil will help kill off some bacteria, and careful pruning of infected areas will often be enough to save the plant.

Neem soil may be safely used every 2 to 3 weeks and work as a preventative measure. This is an excellent natural option for use in conjunction with fungicides.


Geraniums are grown from seed, but often propagation is done with cuttings. Cuttings are susceptible to invasion by numerous soil-borne organisms, and thus, treatment of cuttings with a fungicide is often necessary.

Pythium is a natural inhabitant of the soil and can survive there indefinitely as well as in dirt and debris in the greenhouse. 

It’s essential to let the soil dry out, but you may wish to temporarily pot your geranium or move it to a fresh pot while it recovers. 

Carefully uproot the plant and remove any remaining soil from the roots.

Check for signs of root rot and cut away infected roots.

Dust the roots with a fungicidal powder and plant them in fresh, uncontaminated soil.

You will also need to prune away severely infected stems.

Reintroduce garden specimens to the garden after recovery.

Final Tips: Prevention

Stem rot is a severe and highly contagious disease. Several viruses are known to affect geraniums. They cause mosaic patterns, mottling, crinkled or cupped leaves.

  • When pruning, always sterilize your equipment before work and after every cut.
  • Wash your hands before moving on to the next plant. 
  • Venting and heating should be done in such a way as to reduce the relative humidity and prevent the formation of dew on the leaves and flowers.  
  • Securely dispose of the debris to ensure any unnoticed pest or disease issues don’t spread.
  • Water your geraniums using the soak-and-dry method, and avoid using a hose or sprayer when possible.
  • Instead, water the ground directly to avoid getting the stems or leaves wet.
  • Stick your finger in the soil to determine if it’s time to water instead of relying on a calendar.
  • Neem soil soaks in regular watering can help boost the plant’s defenses against internal infections such as stem rot.
  • Never reuse the soil of an infected plant unless it’s been adequately sterilized.

In some cases, sterilization may be a simple matter of drying the soil out entirely and heat-treating the soil to kill off any diseases. Then, amend the soil to replace any lost nutrients and destroyed organic components.

But, most sterilization treatments are expensive and may need to be done professionally.

For potting soils, discard the infected soil and treat the pot with bleach and hot water or soak it in rubbing alcohol to kill it before reusing.

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