The rank of species from the most abundant to the least was Nigrospora, SH2, SH1, Coniothyrium sp. and A. flavus respectively. Low species diversity of chili plants may be related to high rate of fungicide frequency application in this area (once per week). Gaitan et al. (2005) noted that fungicide application reduced the diversity of endophytic leaf fungi of a tropical tree Guarea guidonia L.