Tomatoes are a staple of the home garden, but the appearance of black spots on the fruit or foliage signals underlying issues that threaten the health and yield of plants. Properly identifying the specific cause is the first step toward effective treatment and protecting the harvest. The causes of black spots are generally divided into infectious diseases, caused by pathogens, and physiological disorders, related to environmental factors or nutrient imbalances. Both categories require different approaches to management and prevention.
Pathogens Causing Black Spots
Infectious black spots on tomato plants are frequently caused by fungal or bacterial pathogens that thrive in warm, humid conditions. Early Blight, caused by the fungus Alternaria linariae (formerly A. solani), typically begins on the older, lower leaves of the plant. The lesions are dark brown to black and can grow up to half an inch in diameter, often displaying characteristic concentric rings that resemble a bullseye or target pattern.
The fungus also affects the fruit, where it creates sunken, leathery, dark spots near the stem attachment point, which may also exhibit the target pattern. Another common fungal issue is Septoria Leaf Spot, distinguished by smaller, circular spots with dark margins and gray or tan centers. These spots typically appear first on the lower leaves, eventually causing the entire leaf to yellow and drop off, although the fruit itself is rarely infected.
Bacterial Spot, caused by the Xanthomonas bacteria, presents as tiny, water-soaked, dark specks on the leaves, stems, and fruit. On the leaves, these spots may be surrounded by a yellow halo, and on the fruit, they develop into slightly raised, brown to black scabby lesions. All of these pathogens survive the winter on infected plant debris or in the soil, ready to infect new plants when conditions are favorable.
Environmental Factors and Physiological Disorders
Black spots that appear on the fruit but not the foliage are often symptoms of a non-infectious physiological disorder. The most common of these is Blossom End Rot (BER), which presents as a dark, sunken area on the blossom end of the fruit. This disorder starts as a small, water-soaked spot that expands into a dry, leathery, brown-to-black patch as the fruit matures.
Blossom End Rot is a localized calcium deficiency within the developing fruit. The disorder occurs even if there is sufficient calcium in the soil because the element is not highly mobile within the plant. The primary trigger is an inconsistent water supply, where periods of drought followed by heavy watering disrupt the plant’s ability to move calcium to the actively growing fruit cells.
Inconsistent soil moisture, root damage, or a highly acidic soil pH (below 6.2) can restrict the uptake of calcium, leading to the development of BER. While the disorder is not caused by a pathogen, the damaged tissue can sometimes become covered with a secondary black mold. Another non-infectious cause of dark blemishes is sunscald, which occurs when fruit is suddenly exposed to intense sunlight after the loss of protective foliage. The resulting damage appears as a white or yellowish patch that can later turn dark and leathery due to secondary infection.
Treatment Strategies and Future Crop Protection
Control of infectious diseases requires removing and disposing of all infected plant material promptly, especially the lower leaves where fungal spores often initiate. Prune with clean tools and avoid working with wet foliage, as water easily spreads spores and bacteria. For active fungal infections like Early Blight or Septoria Leaf Spot, a fungicide containing copper or chlorothalonil can be applied to protect uninfected leaves. Bacterial Spot is managed with copper-based sprays, which primarily work to protect new growth rather than curing existing infections.
Addressing Blossom End Rot and other physiological issues requires correcting the underlying environmental conditions. The most effective action is maintaining consistent soil moisture by watering deeply and regularly, aiming for about 1.5 inches of water per week during the fruiting stage. Applying a layer of organic mulch around the base of the plant helps to regulate soil temperature and moisture, preventing the rapid fluctuations that cause BER.
For long-term crop protection, preventative measures are the most sustainable approach. Always practice crop rotation, avoiding planting tomatoes or related nightshade vegetables in the same spot for at least two to three years, as pathogens can survive in the soil or on debris. Improving air circulation by spacing plants appropriately and pruning lower leaves reduces humidity around the foliage. Finally, a soil test can determine if your soil pH is optimal and if calcium amendments are needed to ensure the nutrient is available to the plants.