Metagenomics, the study of DNA isolated from naturally occurring populations and samples, is rapidly growing. Improvements to cloning and sequencing techniques are allowing researchers to study organism in environmental samples, and new knowledge of species interactions and community dynamics is emerging. The identification of microorganisms in these samples is of vital importance to their interpretation. In the January issue of Cold Spring Harbor Protocols, Annelie Wendeberg of the Helmholtz Centre for Environmental Research presents a protocol for Fluorescence In Situ Hybridization for the Identification of Environmental Microbes. The methods described allow the phylogenetic identification of microorganisms in environmental samples (e.g., water and sediments) by means of fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes followed by signal amplification with catalyzed reporter deposition (CARD). The protocol is one of January’s featured articles, and like all featured articles in Cold Spring Harbor Protocols, it is freely accessible to subscribers and non-subscribers alike.