One of the, if not the most well-known yeast species from Saccharomyces genus is S. cerevisiae, which is not only an indispensable component of numerous fermentation technologies, but also is a model organism in a wide range of scientific fields, including oncology and evolutionary biology. Some strains of S. cerevisiae can even have a more intimate connection to humans as non-pathogenic members of their mycobiota (fungal microbiome). Analogous to the bacterial microbiome, the fungal microbiome and their metabolites also partly determine the overall trajectory of human health or illness. The study of mycobiota is a burgeoning research field and high-throughput sequencing technologies and bioinformatical analysis are just starting to uncover the multifariousness of the fungal world in human bodies. C. albicans is known to be the most prevalent yeast colonizer of the gut flora of healthy adults in industrialized Western countries. By contrast, in a small cohort of Amerindians living in French Guiana, South America, the C. albicans carriage is oddly low and their intestines is predominately populated by S. cerevisiae and C. krusei. Authors who originally reported this peculiar commensalism, conducted genetic analysis and phylogenetic tracking on C. albicans and C. krusei, however, concerning French Guiana S. cerevisiae mysteries remained. Here, using FG S. cerevisiae WGS data, we evaluated the types of genomic variations and their extent in this yeast population. In addition, their genomes were scanned for potential introgressive hybridizations from other species; we attempted to detect traces of gene movements from other members of Saccharomyces “sensu stricto” species into to the gene pool of FG isolates. Identification and characterization of these genomic variations provide a better insight into the lifestyle and microevolutionary history of FG S. cerevisiae and also, set the stage for upcoming investigations.