Humans have used S. cerevisiae to make alcoholic beverages for at least 5000 years and now this super-model research organism is central to advances in our biological understanding. Current models for S. cerevisiae suggest that its population comprises distinct domesticated and natural groups as well as mosaic strains, but we generally know little of the forces which shape its population structure. In order to test the roles that ecology and geography play in shaping the S. cerevisiae species we examined nine variable microsatellite loci in 172 strains of S. cerevisiae isolated from two spontaneous grape juice ferments, soil, flowers, apiaries and bark in New Zealand. Bayesian analysis shows that the S. cerevisiae in NZ comprise a subdivided but interbreeding population that out-crosses ∼20% of the time. Some strains contributing to spontaneous ferments cluster with NZ soil/bark isolates, but others cluster with isolates from French oak barrels. It seems some strains have been globally dispersed by humans in oak barrels while some are locally vectored by insects. These data suggest geography is more important than ecology in shaping S. cerevisiae's population structure.