Blossom-end rot is a common disease of many different plants including peppers of all types, eggplants and tomatoes. Unlike many plant diseases caused by fungi that invade the plant tissue, blossom-end rot is believed to be caused by a combination of improper watering, drought stress, incorrect pruning technique and calcium deficiencies in soil that interfere with the plant's water uptake.
The name of this disease gives a clue to its most obvious symptom -- the blossom end of the peppers first show a small, water-soaked spot that turns black and grows in size. The lesion sinks into the pepper and turns black and leathery, in severe cases covering over half of the pepper and rendering it inedible. At this point, the pepper is susceptible to secondary pathogens that invade the rotted area and can spread to other peppers and plants.
Control methods begin with careful growth practices. Pepper plants enjoy a soil pH of around 6.5; adding lime to soil before growing peppers can keep this soil pH consistent and can add enough calcium to the soil to offset deficiencies that are responsible for blossom-end rot. Use nitrate fertilizer as a nitrogen source as opposed to other kinds of nitrogen fertilizer. Give the peppers a consistent water supply using proper irrigation and mulching. A recommended watering schedule is highly dependent on both the type of pepper being grown and on the unique climate in which the peppers are growing.
Since blossom-end rot is a physiological rather than a fungal disease, there is no treatment that can save peppers once they have succumbed to blossom-end rot. Never eat peppers that come from a plant infected with blossom-end rot. Discard them and adjust fertilization, irrigation and other plant-care practices in successive growing seasons so that future pepper crops do not succumb to the disease as well.