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Yeasts constitute a dietary source for the spotted wing drosophila (SWD) and produce compounds that attract these flies. The study of the chemical composition of the yeast communities associated with SWD should therefore help to understand the relationship between the biology of the insect and the yeast’s metabolism. In the present study, the lipidome of five yeast species isolated from grapes infested by SWD (three <i>Hanseniaspora uvarum</i> strains, <i>Candida</i> sp., <i>Issatchenkia terricola</i>, <i>Metschnikowia pulcherrima</i> and <i>Saccharomycopsis vini</i>) and a laboratory strain of <i>Saccharomyces cerevisiae</i> was explored using an untargeted approach. Additionally, the lipid profile of two species, <i>S. cerevisiae</i> and <i>H. uvarum</i>, which were reported to elicit different responses on SWD flies based on feeding and behavioral trials, was compared with a chemical enrichment approach. Overall, 171 lipids were annotated. The yeast species could be distinguished from each other based on their lipid profile, except for the three strains of <i>H. uvarum,</i> which were very similar to each other. The chemical enrichment analysis emphasized diversities between <i>S. cerevisiae</i> and <i>H. uvarum</i>, that could not be detected based on their global lipid profile. The information concerning differences between species in their lipidome may be of interest to future entomological studies concerning the yeast-insect interaction and could help to explain the responses of SWD to diverse yeast species.