Microbes within complex communities show quite different physiology from pure cultured microbes. However, historically the study of microbes has focused on single species in pure culture and most of microbes are unculturable in our labs, so understanding of complex communities lags behind understanding of pure cultured cells. Methodologies including stable isotope probing (SIP), a combination of fluorescence in situ hybridization (FISH) and microautoradiography (MAR), isotope micrarray, and metagenomics have given insights into the uncultivated majority to link phylogenetic and functional information. Here, we review some of the most recent literatures, with an emphasis on methodological improvements to the sensitivity and utilities of these methods to link phylogeny and function in complex microbial communities.