The technology is now in place for major advances in the genetics and cytogenetics of fishes at the molecular level. One promising method with broad application is fluorescence in situ hybridization (FISH). Methodologies of FISH and the current and potential uses of these chromosomal techniques in fish genetics are reviewed. Highly repetitive ribosomal genes (rDNAs) and the multicopy genes for histones have been localized in several fish species and are providing new information on the evolution of salmonid genomes. Microdissection techniques such as those used to examine the Y chromosome of lake trout can produce paint probes useful in determining chromosomal arm homologies between closely related species. Repetitive sequences isolated from various fish species have been localized to centromeres, telomeres, and sex chromosomes. Some of these are currently being used as species-specific, chromosome-specific or sex-specific probes in aquaculture of fishes. Centromeric and telomeric probes have been used to examine intraspecific chromosome rearrangements such as the transposition of rDNA. Similarly, these types of probes could be used as genome markers for examining interspecific hybrids and in the study of nuclear organization (i.e. the spatial arrangement of chromosomes in interphase cells and gametes) Chromosome mapping of single copy genes, microsatellite loci and syntenic gene groups is now possible with FISH techniques and will be useful in isolating quantitative trait loci (QTL) of importance in aquaculture.