Fruit rots on tomato result from the spread of fungal and bacterial diseases that occur on the leaves and stems over the course of the season. This appears to be anthracnose on the fruit, caused by a fungus called Colletotrichum. It will spread and become darker and more sunken. You can eat the rest of the tomato except for an area around these beginning spots. However, once it spread more, the tomato may not be edible and sweet.
Control leaf spots by avoiding overhead water and picking off lower affected leaves. Here is a fact sheet we developed for diseases of garden tomato.
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