In order to develop a method for discrimination of Corynespora cassiicola isolates pathogenic to sweet pepper among Japanese isolates, this study analysed pathogenic variations of 64 Japanese isolates of C. cassiicola on perilla, cucumber, tomato, aubergine and sweet pepper, and their multigene phylogeny. Japanese isolates were divided into seven pathogenicity groups (PG1–PG7). The virulence of isolates in PG1–PG5 was restricted to perilla, cucumber, tomato, aubergine and sweet pepper, respectively. Isolates in PG6 were virulent to sweet pepper, tomato and aubergine. Isolates in PG7 were avirulent to all tested plants. Multigene phylogenetic analysis of the isolates based on β-tubulin, translation elongation factor 1-α, calmodulin and actin genes showed three divergent clusters, MP-A, MP-B and MP-C. These clusters included all isolates in PG1, PG2, PG8 and PG9 (MP-A), PG3 and PG5 (MP-B) and PG4 and PG6 (MP-C). Isolates in PG7 were distributed amongst all clusters. Furthermore, random amplified polymorphic DNA (RAPD) analysis using universal primers, Q17 (5′-GAAGCCCTTG-3′) and Q13 (5′-GGAGTGGACA-3′), facilitated discrimination of isolates virulent on sweet pepper amongst isolates in MP-B and MP-C, respectively. Together, a combination of the multigene analysis and the RAPD technique allowed the discrimination of the isolates virulent to sweet pepper.