Studies of the genetic mechanisms underlying metabolic storage have focused on a few model organisms. Although very fruitful, these studies have not allowed for the examination of mechanisms across a phylogenetic spectrum. The exploration of natural patterns of metabolic pool size variation across species will help us to better understand the genetics of metabolic adaptation. We examined the metabolic pools size (triglyceride, glycogen and protein) at two ages in 12 Drosophila species with distinctly different ecologies for which complete genome sequences (for 11 of the 12 species) are known. Overall, there were significant differences across species for all three pools, while age and sex appear to affect some metabolic pools more than others. After correcting for the phylogenetic relatedness of the species used, we observed no association between triglyceride and glycogen content. Although within species these two pools sometimes are correlated, at a larger phylogenetic scale control of triglyceride and glycogen contents may have been shaped independently by natural selection.