Habitat selection expressed as oviposition site preferences (OSP), is one component of the complex of behaviours of females seeking a place to oviposit. Drosophila buzzatii females lay their eggs in cactus necroses (rots), where the alternative oviposition sites are patches of adjacent or even partially mixed growing yeast species. The OSP exhibited by individual females is not absolute, but subject to environmental effects and the physiology of the fly, and may vary depending on the particular combination of yeast species present in a rot. Nevertheless, we have shown that OSP of D. buzzatii females is heritable, with evidence from variation among isofemale lines, direct estimation of heritability, generation means analysis and short term selection. Further, this genetic variation appears to be ubiquitous, polygenic and largely non-additive for all yeast species combinations. The consequences of such genotype-specific habitat selection for the maintenance of genetic variation are considered by an evaluation of our results in comparison with assumptions of models of habitat selection. As all assumed mechanisms of these models are apparently met, OSP for yeast species would seem to be a powerful force for the maintenance of genetic variation, and not only at loci affecting the choice of oviposition sites.