Further molecular identification based on 18 S rDNA resulted that SH1 similar (99%) to Accession FJ524323 of GeneBank refer to Unculture endophytic fungus clone R3-63, obtained from wild rice root in China (Yuan et al. 2010) (Table 2). SH2 was similar to Accession No FJ612897 of GeneBank, Fungal sp ARIZ B031, endophytic fungus of tree Cecropia insignis (U’Ren et al. 2010). 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.