Respected sir I am a Ph.D student in dpt. of Vegetable Science at UHF Nauni-Solan. I am working on tomato & I have also seen many cracked fruits during my research trial. Its either due to heavy rains after a prolonged dry period or due to Boron defficiency. I think similar is the case with chilli fruit cracking. So i suggest borax spray on your chilli crop vis a vis maitain optimum moisture level in soil during whole growing period of crop.

Hi Dr. Shrestha 

the crack is probably due to strong fluctuations in temperature and / or drought.

I agree with the previous comments linking the cracking with temperature and water supply fluctuation. But I suggest that you pay attention to the genetic control of this trait, what means that you can select the genotypes that are less susceptible to this disorder. 

Обычно такая проблема связана с режимом полива. Если после долгой засухи полить растения обильно, то плоды часто трескаются. Это же самое случается с плодами томатов, с кочанами капусты. Интересно, что такое случается гораздо реже у баклажан.

In English:

Usually, this problem is related to the regime irrigation. If, after a long drought to water the plants copiously, the fruit often crack. The same thing happens with the fruits of tomatoes with cabbages. Interestingly, this happens much less often in eggplant.

Thanks Ivan. But i don't think it is related to water regime because there was no long drought. Plants received water supplements regularly as and when needed.

I also observe many cracked pepper fruits in this vegetation period and I think that the reason is that in Bulgaria this year was with unusually many pouring rains. Nevertheless I agree with Dr Lopes that we must pay attention and select fruits without cracks.

Dear Dr Gyan, it is important to mention that how many varieties had you grown, was there cracking in all the varieties and at which maturity stage cracking appeared