Chili pepper (Capsicum frutescens) is one species of Solanaceae family that is very popular in Indonesia and some other tropical countries because of its pungency. Chili pepper is an important spice in Indonesia and is also eaten fresh as a pickle to increase appetite. In Indonesia, there are various local names for chili pepper includingcabai, cengek, lombok, pedesan etc. These varied local names represent the various morphological shapes of the chili pepper fruit. We have investigated the variability of some chili cultivars based on morphological characteristics, molecular markers, pungency, and capsaicin content. Some biological facts, such as the tendency of chili pepper to outbreed, have also been found. In this paper, the source of variability and the possible mechanism of increasing genetic variability of Indonesian local chili pepper are also discussed.