Some isolates of Metarhizium anisopliae sensu lato with large conidia (MALC), which was formerly known as M. anisopliae var. majus, from a scarabaeid host, such as isolates from the coconut rhinoceros beetle (Oryctes spp.), have a narrow host range and are particularly adapted to their original host. Despite recent taxonomic revisions of the genus Metarhizium on the basis of DNA sequences, variations in host preferences of MALC have not been linked to DNA sequence variations. This study focused on the phylogenetic status and pathogenicity of MALC isolated from the fruit beetle larva Protaetia orientalis submarumorea (Pos) in Japan to investigate the relationship between virulence and nucleotide sequence variation among MALC. On the basis of the results of the phylogenetic analyses of DNA sequences from five loci, we identified an isolate from Pos (Hn1) as M. majus, which comprised many isolates with large conidia from scarabaeid insects. In the virulence assay of genetically diverse Metarhizium isolates, only Hn1 and its most closely related isolates from soil showed pathogenicity to Pos; however, these Pos-pathogenic isolates showed weak virulence against silkworms. In the analysis of the intergenic spacer region of rDNA, the Pos-pathogenic isolates displayed unique sequence variation and were clearly distinguished from closely related lineages, including isolates from Oryctes sp., which formed a separate monophyletic group. These results indicate that the Pos-pathogenic isolates from Japan are particularly adapted to Pos and can be genetically distinguished from M. majus isolates from different scarabaeid insects.