We assessed the utility of stable isotope analysis as a tool for understanding community ecological structure in a species-rich clade of scincid lizards from one of the world's most diverse lizard communities. Using a phylogenetic comparative framework, we tested whether δ15N and δ13C isotopic composition from individual lizards was correlated with species-specific estimates of diet and habitat use. We find that species are highly divergent in isotopic composition with significant correlations to habitat use, but this relationship shows no phylogenetic signal. Isotopic composition corresponds to empirical observations of diet for some species but much variation remains unexplained. We demonstrate the importance of using a multianalytical approach to questions of long-term dietary preference, and suggest that the use of stable isotopes in combination with stomach content analysis and empirical data on habitat use can potentially reveal patterns in ecological traits at finer scales with important implications for community structuring.