Cryptococcosis in México is caused by both species of the Cryptococcus species complex i.e., Cryptococcus neoformans and C. gattii. The current study was aimed to determine genetic variability of 72 Mexican clinical isolates using PCR-fingerprinting with the primer M13. PCR fingerprinting revealed 55 VNI, five VNII, three VNIII, one VNIV, two VGI, two VGII, two VGIII and two VGIV isolates among those studied. The results show that most cryptococcosis cases in México are AIDS related and are caused by C. neoformans var. grubii, genotypes VNI and VNII. In addition this study revealed for the first time the presence of genotypes VNIV and VGII among Mexican clinical isolates. The present data show that all genotypes that have been described for the Cryptococcus species complex are found in México, indicating a much wider geographic distribution of genotypes than previously reported. The molecular analysis of Mexican cryptococcal isolates generated PCR-fingerprinting patterns which will provide references for future typing studies to allow the integration of Mexican cryptococcal genotypes into the ongoing global genotyping study of the Cryptococcus species complex.