Clinical isolates of the fhngal respiratory and systemic pathogen Histoplasma capsum have been placed in several different classes by using genomic restriction fragent length polymorphisms (RFLPs), but in general have not been distinguished further. We report here that a polymerase chain reaction (PCR)-based DNA fingerprinting method that has been termed arbitrary primer or random amplified polymorphic DNA (RAPD) PCR can distinguish among isolates in a single RF1LP class. In this method, arbitrarily chosen oligonucleotides are used to prime DNA synthesis from genomic sites that they fortuitously match, or almost match, to generate strain-specific arrays of DNA frgments. Each of 29 isolates of RFLP class 2, the group endemic in the American Midwest, was distinguished by using just three arbitrary primers. In contrast, laboratory-derived S and E colony morphology variants of two strains were not disfinguished from their R parents by using 18 such primers. Thus, the clinical isolates of H. capsua are quite diverse, but their genomes remain stable during laboratory culture. These outcomes suggest new possibilities for epidemiological analysis and studies of fungal populations in infected hosts.The fungal respiratory and systemic pathogen Histoplasma capsulatum grows in rich soils and rotting organic matter in moist temperate and tropical regions around the world and infects humans and animals when they inhale its conidia or hyphal fragments (for reviews, see references 4, 6, 16, and 24). Once inhaled, the fungus changes from a free-living mycelium to a host-adapted yeast form, is ingested by pulmonary macrophages, proliferates within them, and spreads to other tissues as the macrophages migrate. A disseminated, often life-threatening form of disease occurs in immunodeficient persons, including those with AIDS and various cancers, very young children, and elderly people, and in those with pulmonary lesions such as are caused by heavy smoking. Infections of immunocompetent people may cause mild influenza-like symptoms or be clinically inapparent, but they can also result in long-term carriage of the organism and a potential for reactivation years after the initial exposure. In these infections, activated macrophages ingest the fungal cells and suppress their growth (unlike nonactivated macrophages) but do not eradicate them completely; calcified lesions also form in the lungs and other tissues, probably because of localized fungal growth and then restriction by host defenses. Survival of fungi in calcifications and in macrophages and other cell types would contribute to long-term latency (4).An ability to distinguish individual strains of H. capsulatum with sensitivity and ease would contribute to epidemiological studies and analyses of infection mechanisms. in mitochondrial DNA and in several nuclear genes allowed H. capsulatum isolates to be divided into six "classes" that seem to reflect geographical distribution or virulence levels (7,(19)(20)(21). In particular, most isolates from immunocompetent adults in the Am...