Mucosal candidiasis is a common complication of HIV infection and HIV- positive women may develop both oropharyngeal and vaginal disease. Colonization with Candida albicans and related species at either site is a common preceding event in asymptomatic women. To examine the molecular epidemiology of colonizing yeast strains in HIV-positive women, concurrent oropharyngeal and vaginal cultures were obtained from 32 women (mean CD4 count 392 cells/mm3, range 0-1319). Positive oropharyngeal cultures were obtained in 18 (56%) and positive vaginal cultures in 10 (31%). Candida species were isolated from both sites simultaneously in nine (28%) women. All strains were evaluated for restriction fragment length polymorphisms (RFLPs) at the ribosomal DNA locus (using a heterologous 8.4-kb NotI probe from H. capsulatum) and with a C. albicans-specific repetitive DNA probe. Isolates were grouped into three classes by the NotI probe and then members of each class were evaluated with the C. albicans-specific probe. Isolates were subsequently evaluated by random amplified polymorphic DNA (RAPD) PCR with four arbitrary primers to detect strain-specific differences. All isolates tested were unique and could be discriminated by RFLP or RAPD PCR. Vaginal and oropharyngeal isolates from the same individual in all nine cases were dissimilar, suggesting that the dominant strain of Candida colonizing different body sites is different. These findings suggest that the epidemiology of Candida infection in HIV disease is complex, that the development of oropharyngeal and vaginal disease may be disassociated, and that HIV-positive patients are each infected by their own unique strains of Candida.