When black seeds in tomato fruits are found, the situation can be worrying for many gardeners as this can mean unhealthy fruits. A tomato with black seeds can be perceived apprehensively because the condition does not seem ordinary, especially when there are black spots inside tomatoes.

A Close Shot Of Tomato

We need to first understand what these dark tomato seeds are so we can make steps to prevent any future occurrence of dark seeds in tomatoes.

In this article, we’ll shed light on this strange occurrence and share some expert tips and tricks to prevent this from happening to you.

Why Are My Tomato Seeds Black?

There are several possible reasons as to why your tomato seeds are black, some of which are overripe tomatoes and blossom end rot. While dark tomato seeds are not visually appealing for many consumers, they present very little harm and should not be a huge cause of alarm. The dark seeds in tomatoes merely reflect the overall health condition of the plant and its environment.

The natural color of healthy common-variety tomato seeds is a greenish yellow. However, there are times when the seeds end up darker, with shades ranging from brown to black.

If the tomato itself does not show any visible symptoms of disease, decay, foul odors and other disagreeable characteristics, it may still be considered edible.

There are some theories regarding the causes of the seeds of the tomato turning dark. Let’s go through them and determine which one could be causing your tomatoes to have dark seeds.

– Over-ripened Tomatoes

An overripe healthy tomato may produce dark seeds most of the time. The dark color of the seeds indicates that they are ready for germination.

In some cases, the dark seeds in tomatoes end up sprouting inside the fruit. This process is called vivipary and this occurs more often than you may think. You can even find overripe tomatoes bursting with cotyledons, which are the first set of growing leaves.

Unripe tomatoes contain a plant hormone called abscisic acid which prevents the seeds from germinating while inside the fruit. As the tomato slowly ripens, the abscisic acid level slowly tapers off, encouraging the seeds to darken and sprout.

The tomato fruit is inclined to reproduce naturally through its seeds. An overripe tomato provides the best germinating conditions through its high internal moisture content, which is the ideal environment to promote optimal seed germination.

– Blossom End Rot (BER)

Blossom end rot is one of the most common diseases that plague tomatoes. The most visible symptom of a tomato inflicted with BER is a dark spot that can be seen on the bottom of the fruit. This spot is where the blossom was originally located.

The dark spot can begin to rot, which slowly affects the seeds inside, turning them dark. This can be quite unsightly and many gardeners discourage the consumption of tomatoes with BER symptoms. Some gardeners recommend removing the dark parts since the healthy part of the tomato can still be consumed safely.

Some studies show that BER occurs due to the inability of the tomato plant to take sufficient calcium from the soil at an appropriate rate. Some researchers also theorize that BER can be due to irregular watering schedules.

The dark seeds in tomatoes can also be a result of internal BER, which occurs when the fruit experiences BER symptoms but does not display any external signs. Under this condition, some gardeners advocate removing the blackened seeds and consuming the tomato as usual. Some take a more guarded stance and discard the fruit entirely.

Black seeds on my tomato

– Other Causes

Some tomatoes have predisposed genetic mutations that can cause their seeds to naturally darken without any illnesses or diseases as the cause.

It is also common to find a few black seeds in perfectly healthy tomato fruits. A possible cause for these few seeds to darken is that they were unable to receive essential nutrients while growing.

What Causes Blossom End Rot (BER)?

BER is usually caused by calcium deficiency and inconsistent watering. To prevent BER from occurring, it is most ideal to ensure that your tomato plant receives the appropriate amount of calcium as well as regular watering.

– Can Overwatering Cause BER?

Irregular watering causes BER. Overwatering may cause the root system of the tomato plant to drown, making it rot and perish. A regular watering schedule with an appropriate amount of water is the most ideal for the prevention of BER.

– How Can We Prevent BER?

BER can be avoided by ensuring that the tomato plant receives the correct amount of essential nutrients, especially calcium, along with a regular watering schedule.

Mulching can help prevent the soil from drying out and provide moisture to the root system of the plant. A layer of straw, compost or grass mulch conserves soil moisture during the hot and dry periods. Mulches ensure a more frequent presence of water, which helps prevent BER.

Foliar fertilizer applications of liquid calcium solutions can also enhance the overall health of your tomato plant. The supplemental calcium nutrient can correct and prevent BER from occurring as long as the dosage is according to instructions. However, take note that too much fertilizer applied at one time can also encourage BER. An appropriate balanced amount, as well as regular fertilization activities, can greatly reduce the incidence of BER.

– Care

Most tomatoes prefer to grow in slightly acidic soil. Ensuring that the plant grows in the ideal soil pH level of 6.2 to 6.8 can help prevent BER from occurring.

Several tomato plants can exhibit signs of BER when their soil is too cold. To raise soil temperatures, some gardeners use protective black or red plastic coverings to ensure a more regular soil temperature.

The root system of the tomato plant can become sensitive to damage if the roots experience trauma. It is best to avoid digging around the base of the plant where the roots may be located.

– What To Do if Your Tomato Plant Develops BER

Once any visible sign of BER is spotted, it is advisable to remove the entire fruit completely by cutting it off from the plant. Some varieties of tomatoes can be quite susceptible to conditions that cause BER, especially the heirloom ones.

BER in fruits is incredibly difficult to reverse once it has started, so the best solution is to remove the unhealthy plant as soon as possible.

Tomatoes with visible signs of BER can become entry points for bacterial and fungal infections, which can infect and spread to other fruits and plants. Some plant varieties of tomatoes can be less prone to BER, and these could be planted instead of other varieties such as heirlooms.


Is It Safe To Eat the Black Seeds Inside Tomatoes?

The short answer is yes, it is safe to eat the black seeds inside tomatoes, but it also depends on your preference and level of comfort. While the sight of black seeds inside tomatoes can be jarring for some consumers, many have eaten the fruit without any harm. A lot of people are of the opinion that as long as the tomato has no unpleasant taste or smell and is not obviously diseased, the fruit may still be consumed safely.

While some people prefer to remove the black seeds prior to consuming them, others prefer to consider tomatoes with black seeds as entirely unfit for consumption and throw them away.

Solution for black seeds in tomatoes

– Can You Still Eat Overripe Tomatoes?

Yes, but it is best to consume tomatoes that are perfectly ripe to ensure optimal visual and gustatorial satisfaction. Overripe tomatoes may not be the most ideal fruits to consume, especially when there are other choices that are better. However, while the taste and texture of overripe tomatoes can be off-putting for some, others find them quite enjoyable.

– Is It Safe To Eat Tomatoes With Signs of Vivipary?

While the sight of germinating seeds sprouting from the tomato can be a little discomfiting for some, it is generally safe to eat tomatoes with vivipary conditions. Vivipary occurs due to excess nitrogen fertilization, potassium deficiency, high moisture content and a decline in abscisic acid levels. Lower temperatures can also hasten the vivipary process.

Although it is generally safe to eat, it is still advisable to completely disregard the consumption of tomatoes with signs of vivipary. Aside from the visual uneasiness that most people experience, some reports state that the sprouts of tomato seeds may possibly be toxic for some people.

It is recommended to err on the safe side and avoid eating tomatoes with obvious signs of vivipary.

Two Slice of Tomatoes


Can you use tomatoes with black seeds for sauce?

Yes, tomatoes with black seeds can be used for sauce, as the seeds don’t affect the flavor or texture significantly.

Does tomato blight cause it to have black seeds?

Tomato blight doesn’t directly cause black seeds; it primarily affects foliage and fruits, causing rot and blemishes.

Do tomatoes with anthracnose have black seeds?

Anthracnose-infected tomatoes may develop black lesions, but the seeds are not typically affected.


Black seeds in tomato fruits can happen more often than we think. More often than not, Blossom End Rot (BER) can be a sign that our tomato plants need more attention than we previously thought.

  • Dark tomato seeds can be a result of overripe fruits, which have low abscisic acid levels that encourage them to blacken for germination.
  • Dark seeds in tomatoes can also be attributed to internal BER, which is an indication of calcium deficiency and inconsistent watering.
  • BER can be prevented in several ways, such as by ensuring a regular supply of essential nutrients, consistent watering, plant variety selection, and correct soil conditions.
  • A tomato with black seeds may still be consumed, although it is best to remove the seeds prior to consumption or discard the fruit entirely for a safer gustatory experience.

Gardeners who find black spots inside tomatoes are recommended to be more vigilant in ensuring their plants receive better care. With some appropriate foliar applications, regular watering, and ideal soil conditions, it should be easy to prevent dark tomato seeds from occurring again.

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