Paracoccidioides brasiliensis is the etiologic agent of paracoccidioidomycosis (PCM), the most important systemic mycosis in Latin America. The armadillo Dasypus novemcinctus has been confirmed as the first natural reservoir of this fungus and its geographic distribution is similar to the distribution of human PCM. This work analysed the virulence profiles and genetic diversity of P. brasiliensis isolates from different armadillos and clinical isolates. The animal isolates were obtained from the Botucatu endemic area of PCM, with exact information of the collection sites. The clinical isolates, except Pb265, were obtained from patients that live in the same endemic area (Pratânia, Manduri and Botucatu county). Virulence was evaluated in an experimental hamster model by colony-forming units (CFU) and histopathological analysis in the testis, liver, spleen, lung and circulating specific antibodies measured by ELISA. Molecular characterisation was evaluated by RAPD methods and sequencing analyses of the internal transcribed spacer regions (ITS 1 and ITS 2) and 5.8 S ribosomal gene. All isolates from armadillos were virulent, with dissemination to many organs. The clinical isolate Pb 265 was less virulent. The isolates were classified into four categories according to number of CFU per gram of tissue: very high, high, intermediate and low virulence. Molecular analysis showed large genetic similarity between all isolates and did not separate armadillos from clinical isolates. This study confirms that armadillos harbor pathogenic genotypes of P. brasiliensis, probably the same ones that infect man. Thus, the armadillos are very important animals in the epidemiology this disease.