This protocol presents methods for 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). In this procedure, FISH probes are conjugated with the enzyme horseradish peroxidase (HRP). After hybridization, the subsequent deposition of fluorescently labeled tyramides results in substantially higher signal intensities on target cells than after FISH with probes labeled directly with fluorochromes. This protocol describes the custom labeling of tyramides with different fluorochromes, as well as sample preparation and cell permeabilization strategies for various microbial cell wall types. A protocol for sequential multicolor CARD-FISH for the simultaneous detection of different phylogenetic groups is also presented.