Are you overwatering? If not, try some epsom salt foliar spray on the entire plant. This should help some.

Stoney

It could be BER (Blossom End Rot). It usually means you need to add calcium to your soil.

It could also be Bacterial Soft Rot, caused by too much watering.

Bacterial Soft Rot is caused by bacterium Erwinia carotovora pv carotovora and affects Chile pods. The internal tissue softens before eventually turning into a watery mass with a foul smell. This problem is worst in wet weather because the bacteria are splashed from the ground and onto the fruit. It can also be started by insect injury.

This post was edited by RonnyB123 on Sun, May 11, 14 at 22:19

It looks like BER, if it was on top or middle I would think more on the lines of sunburn/sun scald.

Mark

I couldn't find any insect damage... Not to say its impossible though.

I also didn't realize overwatering could lead to BER, the soil gets plenty of calcium. There was quite a period of overwatering here lately too with rains, looks like BER may indeed be the culprit. Thanks guys. Now I'll just have to hope the others aren't effected, so far it's just this one plant.

Jay