Metagenomics, the study of DNA isolated from samples of naturally occurring microbial populations, is rapidly growing. Improvements to cloning and sequencing techniques are allowing researchers to study microorganisms 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 interpreting the results of such studies. In the January issue of Cold Spring Harbor Protocols (http://www.cshprotocols.org/TOCs/toc1_10.dtl), Annelie Wendeberg of the Helmholtz Centre for Environmental Research (http://www.ufz.de/index.php?en=13987) 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). As one of January's featured articles, it is freely available on the journal's website (http://cshprotocols.cshlp.org/cgi/content/full/2010/1/pdb.prot5366).