Stem-end rot
The infection happens at or before harvest, but the rot only shows once the fruit is softening in storage — by then, prevention at picking time is the only thing that could have stopped it.
- Disease type
- Post-harvest fungal rot complex
- Infection point
- At or before harvest, often via the stem scar
- Symptoms appear
- During ripening in storage or transit
- Main risk
- Fruit loss after it has already left the orchard
Overview
Stem-end rot is a post-harvest disease complex caused by several fungi (commonly Lasiodiplodia theobromae and Colletotrichum species, among others) that infect the fruit at or before harvest, often through the stem scar or minor wounds, but stay latent until the fruit begins to soften and ripen in storage or transit.
Because the infection is invisible at picking, a batch of apparently sound, firm fruit can still develop stem-end rot days later — which is why prevention is built around harvest handling and stem care rather than a spray applied once symptoms appear, by which point the fruit is already a loss.
How to identify it
- Rot beginning specifically at the stem end of the fruit, not at a random point on the skin.
- Darkening and softening that spreads from the stem end through the flesh as the fruit ripens.
- Symptoms are absent or barely visible at harvest — they develop over the following days as the fruit softens in storage or transit.
What causes it and when
- A complex of fungi, most commonly Lasiodiplodia theobromae and Colletotrichum species, that infect the fruit at or shortly before harvest.
- Infection typically enters through the stem scar left when the fruit is picked, or through minor wounds and bruises on the skin.
- The fungus stays latent (inactive) while the fruit is firm and unripe, then becomes active as the fruit's own ripening processes begin — which is why the rot only becomes visible well after picking.
Cultural & organic control
- Harvest with the stem intact where the crop allows it, rather than pulling fruit free and tearing the stem scar.
- Handle fruit gently at every stage — bruises and wounds are entry points for the same fungi that cause stem-end rot.
- Cool fruit promptly after picking; slower ripening gives the latent fungus less opportunity to become active before the fruit reaches the buyer.
- Remove and destroy dead wood, mummified fruit and orchard debris that can carry the fungus over between seasons.
Chemical control
- A pre-harvest fungicide spray timed ahead of picking can reduce infection pressure where the disease has been a recurring problem.
- Once fruit shows stem-end rot symptoms in storage, there is no effective treatment — the priority becomes sorting and removing affected fruit before it spreads decay to healthy fruit nearby.
- Confirm the current recommended product and timing for your crop with your local KVK.
Prevent it coming back
- Treat harvest handling as the main prevention point, since the infection happens at or before picking, well before any symptom is visible.
- Sort and grade fruit promptly after harvest, and cool it quickly, rather than letting it sit in the heat before storage or transport.
- Keep the orchard floor and canopy clear of dead wood and fallen, rotting fruit, which harbour the causal fungi between seasons.
Crops most at risk
Where this problem is called out in our crop guides — open a crop for the full package of practices.
Varieties to consider
Named seed varieties whose resistance or susceptibility to this problem is documented on their own variety page.
Frequently asked questions
My fruit looked perfectly fine when I picked it, so why did it rot from the stem a few days later?
This is the classic pattern of stem-end rot — the causal fungi infect the fruit at or before harvest, often through the stem scar, but stay inactive until the fruit's own ripening process kicks in during storage or transit. By the time the rot is visible, the infection happened days or weeks earlier, which is why gentle handling and prompt cooling at harvest matter more than anything you can do once symptoms show.
Can I treat stem-end rot once I see it in a batch of ripening fruit?
No effective treatment exists once the rot is visible — sort and remove affected fruit promptly to stop it spreading decay to sound fruit nearby, and focus on prevention (careful harvest, gentle handling, prompt cooling) for the next batch.
How is stem-end rot different from anthracnose?
The two often occur together and can even share some of the same causal fungi, but stem-end rot specifically starts at the stem scar and is tied to harvest wounding and post-harvest ripening, while anthracnose more broadly causes sunken spots on the fruit surface, leaves and twigs. Both are managed with the same core practices — careful handling, good orchard hygiene, and prompt cooling after harvest.
Symptoms and control measures follow ICAR, KVK and state agricultural-university package-of-practices; any named chemical is a registered use. Always read the product label and confirm the dose for your crop and zone. editorial policy.