Twenty-eight Candida albicans strains obtained from women with vaginal candidiasis were tested for phospholipase and proteinase production and clustered by multilocus enzyme electrophoresis (MLEE). The proteolytic and phospholipidic activity were considered moderate (0.56 ± 0.12 mm and 0.53 ± 0.09 mm, respectively) for all isolates. The isoenzymes malate dehydrogenase (MDH) and sorbitol dehydrogenase (SDH) showed strong intra-specific discriminatory power. The numerical and genetic interpretation of the bands produced by the isoenzymes tested presented similar discriminatory power. The genetic diversity of the isolates was measured by allelic and genic frequency, perceptual index of polymorphic loci (P = 87.5%), average number of alleles per locus, average number of alleles per polymorphic locus, average heterozygosity observed and average heterozygosity expected. We verified that three isoenzymatic loci (Adh, Gdh and Sdh-2) were not in Hardy–Weinberg equilibrium. A dendrogram constructed based on the genetic distance matrix of Nei showed seven clusters; 57.15% (16) of the isolates were considered highly related or indistinguishable, and 42.85% were considered moderately related or unrelated. We did not find a relationship between the clusters and the exoenzymes production.