One to two millimeters. That is the size of a bacterial speck lesion, one common cause of black spots on tomatoes, barely bigger than a pinhead.
A different cause, bacterial spot, runs four to five millimeters. That is more than double the size, and it is not the only clue worth checking.
Black spots on tomatoes are not one single problem. At least six separate causes can leave a dark mark on a tomato’s skin.
Some of those causes are diseases. Some are insects, and one is not a disease at all.
Sizing up black spots on tomatoes, one cause at a time
A tiny black fleck under two millimeters points toward bacterial speck. It shows up on both green and ripe fruit, often with a faint yellow ring around it at first.
A larger black spot in the four to five millimeter range points toward bacterial spot instead. It is sometimes scabby or slightly raised, and it can carry a white, greasy looking halo early on. That halo fades as the spot matures.
A sunken, circular spot on fruit that is already ripe or overripe tells a different story. That pattern is the signature of anthracnose, a fungal disease that mostly ignores green fruit.
Bacterial speck versus bacterial spot
These two look similar enough to confuse at a glance, but the conditions that cause them barely overlap. Bacterial speck favors cool, wet weather, developing fastest between about 64 and 75 degrees Fahrenheit.
Bacterial spot favors the opposite end of the thermometer. It develops rapidly once temperatures climb to 68 degrees Fahrenheit or higher, according to UC IPM’s bacterial spot pest notes. It slows down again once nights drop below 61 degrees.
Both spread the same practical way. Splashing rain moves the bacteria from one leaf or fruit to the next. Overhead irrigation and handling wet plants do the same job just as effectively.
Neither responds to a fungicide, since both are bacterial rather than fungal. Copper based products offer partial control when applied before infection sets in, not after spots have already formed.
A full breakdown of bacterial spot on tomatoes covers identification and treatment for that specific disease in more depth. It is worth reading before assuming either bacterial disease is the culprit.
Anthracnose, the ripe fruit specialist
Anthracnose lesions start small and sunken, usually less than half an inch across at first. As the spot ages, its center turns black and gets dotted with tiny fungal specks.
Those specks are called microsclerotia, and they are what gives an anthracnose spot its darkest, most distinctive center. Salmon colored spores can also ooze from the lesion in humid weather.
This disease mostly leaves green fruit alone. It waits for a tomato to ripen or overripen before infection really takes hold. That timing is exactly why so many anthracnose spots show up right at harvest time.
The fungus survives in soil debris between seasons, and rain splashes spores up onto low hanging fruit. Rotating away from tomatoes and other nightshade family crops for at least a year helps break that cycle.
Buckeye rot and the fruit touching the ground
Buckeye rot gets its name from a pattern of dark, concentric rings. Those rings resemble the marking on a buckeye seed, starting brown and darkening as the spot spreads.
Fruit resting directly on wet soil is the classic entry point. A lesion can grow large enough to cover more than half a fruit under warm, wet conditions.
Staking or caging a plant to keep fruit off the ground is the simplest fix. A layer of mulch under the plant also cuts down on soil splash reaching low fruit clusters.
When the black spot is not a disease at all
Stink bugs feed by piercing fruit and withdrawing juice. The fruit’s own defense reaction to that wound is what leaves the mark. On green fruit, that shows up first as a dark pinprick surrounded by a lighter halo.
Below the surface, that feeding site can turn corky and pitted as the fruit keeps growing around the wound. Ripe fruit often shows a paler, less obvious version of the same damage.
A more subtle risk rides along with the feeding itself. Stink bugs can carry yeast and other organisms on their mouthparts. Those organisms can cause fruit to rot from that same puncture point.
Checking a plant for the bugs themselves, not just the damage, is the fastest way to confirm this cause. A cluster of dark pinpricks on otherwise healthy green fruit is a strong clue on its own.
The one that is not black at first
Blossom end rot starts out differently than everything else on this list. It begins as a water soaked, tan patch at the blossom end of the fruit, not a black spot. Left alone, that patch often darkens toward black and sinks in as it grows.
By the time it looks black, it can be mistaken for a disease lesion at a glance. The location gives it away every time. Blossom end rot only ever appears at the blossom end, never scattered across the fruit’s side.
A full explanation of blossom end rot covers that disorder, its causes, and how to prevent it. It is a calcium and watering issue, not an infection, so treatment looks completely different from any disease on this list.
Why weather decides which cause shows up
Every disease on this list has a favorite weather pattern. A wet spring pushes bacterial speck first, since it thrives in cool, damp conditions.
A hot, humid summer favors bacterial spot instead. Anthracnose waits even longer, since it needs fruit that has already started to ripen.
That timing pattern is a useful diagnostic shortcut on its own. A spot that appears early in a cool, rainy season points one direction. A spot that shows up on ripe fruit in late summer heat points somewhere else entirely.
Buckeye rot follows its own separate rule. It cares less about air temperature and more about how wet the soil stays around the lowest fruit clusters.
A garden with poor air circulation makes every one of these worse. Crowded plants stay wet longer after rain or watering, giving bacteria and fungal spores more time to establish.
What to actually do about it
Sanitation does more work than any spray for most of these problems. Removing infected fruit helps right away. Cleaning up dropped fruit and debris at the end of the season cuts next year’s starting population too.
Avoiding overhead irrigation slows every bacterial and fungal cause on this list. Watering early enough that foliage dries before evening works nearly as well. Wet leaves and wet fruit are what all of them need to spread.
Crop rotation matters more than most home gardeners realize. Avoiding tomatoes, peppers, and eggplant in the same spot for at least a year helps break the cycle. It starves out soil surviving pathogens like anthracnose and buckeye rot.
A copper fungicide labeled for tomatoes can offer preventive help here. It works best applied before symptoms appear, not after. It will not do anything for stink bug damage or blossom end rot, since neither is an infection.
Resistant varieties and spacing choices that actually help
Some tomato varieties carry genetic resistance to specific bacterial and fungal diseases, and choosing one of those where local disease pressure is high can cut losses before a single spot ever appears. That resistance is usually listed right on the seed packet or catalog page as a short string of letters after the variety name.
Spacing plants further apart than the tag suggests is another simple habit that pays off. Extra air movement between plants dries foliage and fruit faster after rain, which shortens the window every one of these pathogens needs to infect.
Pruning lower leaves that touch the soil removes one more entry point for splashed spores. None of these habits guarantees a spot free season, but together they shift the odds meaningfully in a grower’s favor.
Fruit spots versus leaf spots
Fruit and leaves do not always show the same problem at the same time. A plant can carry a leaf disease with no fruit symptoms at all, or the reverse.
A separate guide to black spots on tomato leaves covers the leaf only patterns in depth. Several of those causes differ from what shows up on fruit. Checking both leaves and fruit together gives a more complete picture than either alone.
A photo run through the site’s free tomato problem identifier tool can help narrow things down. It works well before deciding on any treatment. That extra step is worth it when the visible symptoms could point two or three different directions.
The broader catalog of tomato diseases is worth bookmarking for anything that does not match the patterns described here. Some seasons bring less common problems that a quick fruit spot guide cannot fully cover.
Cracking, sunscald, and catfacing can also leave a fruit looking damaged without a single spot involved. The wider troubleshooting guide for fruit problems in general rounds up those other causes in one place.
Frequently asked questions
What causes small black dots on tomatoes?
Tiny dots under two millimeters, sometimes with a faint yellow ring, usually point to bacterial speck. It favors cool, wet weather and spreads through splashing water and handling wet plants.
Are black spots on tomatoes safe to eat around?
Trimming away a small, isolated spot is generally fine for most of the causes here. The rest of the fruit is safe to eat. A fruit with extensive rot, an unpleasant smell, or soft mushy tissue is better discarded entirely.
Why do only my ripe tomatoes get black spots?
That pattern points toward anthracnose. It mainly infects fruit once it ripens or overripens, rather than while it is still green. Sunken, circular lesions with dark centers are the telltale sign.
Can black spots on tomatoes spread to other fruit?
Yes, for the bacterial and fungal causes. Rain splash and wet handling move spores and bacteria between fruit and plants. Removing affected fruit promptly limits how far a problem spreads through the planting.
How do I tell a disease spot from stink bug damage?
Stink bug damage usually starts as a dark pinprick with a lighter halo on green fruit. It lacks the sunken or scabby texture a disease lesion carries. Finding the bugs themselves near the damage is the clearest confirmation.