This study investigated the distribution of endophytic fungi obtained from the surface sterilized tissues of leaves, stems and roots of chili pepper (Capsicum annuum L.) plants in seedling, flowering and fruiting stages in Korea and their antifungal activity. A total of 481 isolates were recovered and were identified using molecular techniques. Based on rDNA ITS gene sequence and phylogenetic analysis, 21 fungal genera were characterized, belonging to 16 Ascomycota and 5 Basidiomycota. Penicillium in seedling stage, Fusarium in flowering stage, Colletotrichum followed by Fusarium, Alternaria and Xylaria in fruiting stage was predominant and Alternaria, Cladosporium and Fusarium were common in all growth stages. Among 481 endophytes 90 phenotypes were evaluated for the antimicrobial activity against three major pathogens (Phytophthora capsici, Colletotrichum acutatum and Fusarium oxysporum) of chili pepper. Among them 16 isolates inhibited the growth of at least one test microorganisms. Three strains showed a broad spectrum antifungal activity and displayed strong inhibition against chili pepper pathogenic fungi.