Genetic research in fishes is poised to contribute a vast amount of information on the structural organization and function of vertebrate genomes. Recent advances in molecular biology have made possible the widescale characterization of genomes in all living organisms. This includes defining chromosomes at the cytological level down to their linear composition at individual nucleotide base pairs. Pioneering gene mapping studies into the genomes of fishes will only serve as the starting point for more detailed studies into the function of these genomes. Future research directed at understanding the mechanisms of gene actions and interactions will benefit all areas of biology, including ecology, ethology, evolution, and physiology. Gene mapping data from brown trout and rainbow trout are used to exemplify how basic information on gene transmission in a species may help to localize centromeres onto a genetic map and identify chromosomal regions possessing a high degree of segregation distortion. Genetic maps may also be used to identify differences in recombination levels among individuals and between the sexes when multiple mapping families are utilized in studies. Observations of this type are the antecedents to more complex biological investigations on the genetic architecture underlying these phenomena.