We sampled commensal yeasts from three body sites of 24 healthy individuals to examine the patterns of commensal yeast species distribution and strain relatedness within and among individuals. To examine the short-term dynamics, each individual was sampled three times every 35-40 days at each of three body sites: mouth, fingernail, and toenail. The hosts included six genealogically unrelated individuals and 18 that belonged to four families. A total of 63 morphologically distinct colonies were isolated, identified, and genotyped. Nine yeast species were recovered, including 28 isolates of Candida albicans; 26 of C. parapsilosis; 2 each of C. krusei and C. tropicalis; and 1 each of C. famata, C. glabrata, C. guilliermondii, C. lusitaniae and Trichosporon beigelii. A significant difference in total yeast recovery rate between families was observed. However, body sites did not differ in the rates of yeast recovery. The three body sites showed different species distributions with the fingernail sample containing the highest species diversity, followed by the toenail sample. The oral sample contained the lowest species diversity with all 23 oral isolates being C. albicans. Among the 63 strains, forty-six unique genotypes were identified by PCR fingerprinting. Eleven shared-genotypes were identified, seven of which were from the same body site of the same host. The other four were from different members of the same family. Several family-specific genotypes and genotype clusters were found but the results were inconsistent with strict familial transmission of human commensal yeasts. A single host can have multiple species or multiple genotypes of the same species at the same or different body sites. Changes of species and genotypes over the sampling period for the same body site of individual hosts were also observed, including one direct observation of familial yeast transmission between two members of the same family during our sampling period. Our results indicate dynamic processes of yeast colonization, maintenance and evolution in healthy human hosts.