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The cactophilic species, Drosophila buzzatii, normally breeds in decaying pockets of Opuntia cladodes, in which there is a complex interaction with the microbial flora, especially yeast species. Isofemale lines were used to estimate genetic variation among larvae reared on their natural feeding substrate. Four naturally occurring cactophilic yeast species isolated from the same Tunisian oasis as the Drosophila population were used. Two fitness components were studied for each line, viability and developmental time. Genetic variations among D. buzzatii lines were observed for both traits. A significant yeast species x isofemale line interaction for viability was also evidenced, suggesting the occurrence of specialized genotypes for the utilization of breeding substrates. This genetic heterogeneity in the natural population may favor a better adaptation to the patchily distribution of yeasts.