Strains of a human pathogenic yeast, Candida albicans, have (A) intronless, (B) intron‐containing, and (C) a mixture of intron‐containing and intronless 26S rRNA genes. To elucidate the significance of these three genotypes in pathogenesis, we measured two major virulence factors, extracellular proteinase and phospholipase activity, in 56 clinical isolates of C. albicans, and investigated the relationship between genotype and enzymatic activity. The genotype B strains had significantly higher proteinase and phospholipase activities than genotypes A or C. These results suggest that to understand the pathogenesis of C. albicans, the genotypes should be considered.