In this report, strains of five different Candida species (Candida albicans, Candida guilliermondii, Candida tropicalis, Candida krusei, and Candida parapsilosis) isolated from healthy human oral cavities as well as their respective type-strains were used in order to establish the genetic diversity existing among the different species and within a certain species, by the analysis of their electrophoretic alloenzyme patterns. These profiles were analyzed for their band positions in the gels, which allowed to group the strains of the same species in species-specific clusters and to treat them as conspecific populations. A total of thirteen enzymatic loci were obtained (ACO, ADH1, ADH2, CAT, G6PDH, GDH, GOT, IDH1, IDH2, LAP, LDH, PER, and SOD). The allelic frequencies (p) and the heterozygosity (h) for all the thirteen loci were determined by diversity index formulas. The GST index is the estimated proportion of genetic diversity that was applied in order to establish inter and intra populational diversity, which, for our results, indicated that 37.75% of total genetic diversity was attributable to differences among the species and the remaining 62.25% was attributable to differences within these populations. An Euclidian distance dendrogram for the different conspecific populations was built, showing that C. guilliermondii grouped first with C. tropicalis and thus formed a expanded cluster with C. albicans. This cluster combined later with another one composed by C. parapsilosis and C. krusei. Comparing our results to the others that were obtained by different molecular techniques, we have observed that the clustering hierarchies follow different paths of organization, varying according to the methodology employed.