Several different repetitive DNA sequences have been isolated from the pathogenic yeast Candida albicans. These include two families of large dispersed repeat sequences (Ca3, Ca24) and a short (23-bp) tandemly repeated element (Ca7) associated with C. albicans telomeres. In addition, a large subtelomeric repeat (WOL17) has been cloned. DNA fragments containing the telomeric repeats are highly variable among different C. albicans strains. We have shown that the Ca3 repeat is relatively more stable and is suitable for use as a species-specific and strain-specffic probe for C. albicans.Candida albicans and related species are responsible for the majority of oral and vaginal yeast infections (la, 26) and continue to increase in frequency as a major cause of systemic infections in immunocompromised hosts (1,4,5,25,30). Because C. albicans and related species lack sexual cycles (46), genetic studies have been difficult. Analyses of mitotic recombination of auxotrophic markers (47, 48), DNA content (32, 42), and complexity (32) and chromosome organization by orthogonal field alternating gel electrophoresis (21) indicate that C. albicans possesses a diploid genome organized into about eight chromosome pairs (16,20), with a DNA content and complexity similar to those of bakers' yeast, Saccharomyces cerevisiae (17).The lack of a sexual phase in C. albicans and related species presumably prevents opportunities for recombination between strains, leading to a direct clonal relationship in the descendants. This characteristic may be useful in clinical analyses of colonization and epidemiological studies, since it allows direct determination of strain relatedness by employing genomic markers. Distinguishing between species and strains is of paramount importance in such studies, since it has been demonstrated that more than one Candida species and more than one strain of a single species can colonize or infect the same individual (9,23,27,28,44). In addition, multiple "switch phenotypes" (growth forms with distinctive cell types and colony morphologies [40,41]) of the same strain can be found at the same site of infection (43). Sugar assimilation and biotyping methods are normally accurate in distinguishing species and, in many cases, strains (15, 29, 31) but can provide false distinctions between switch phenotypes of the same strain (1). Serological typing methods can discriminate between only two C. albicans subtypes (8). Even electrophoretic karyotyping can be misleading, since subclones of single strains can exhibit significant changes in chromosome size or structure over relatively short periods of culture (36,45 Repetitive DNA sequences provide useful markers for strain identification and also provide keys to understanding chromosome structure and organization. Scherer and Stevens (38) reported the isolation of a dispersed middle repetitive DNA sequence from C. albicans and showed that it could be used for fingerprinting strains of that species. We have also generated species-specific repetitive DNA probes that have been ...