Genetic relationships and distribution patterns among populations, subspecies, and species of northeastern Pacific myxodin clinids were analyzed from allozyme data. The most recent revision recognized six species and 12 subspecies in two genera, Heterostichus and Gibbonsia. Allozymes from 40 gene loci from all 12 nominal taxa were analyzed to compare heterozygosity levels, Hardy-Weinberg equilibrium conformance, genetic distances, and phylogenetic relationships. Sample sites ranged from Carmel, California, to central Baja California, Mexico, and included areas of sympatry, disjunct distribution, and relative isolation. Offshore island sites included the California Channel, San Benito, and Guadalupe islands; the last with several endemic nominal taxa. In addition, morphological characters putatively defining closely related taxa were reexamined because preliminary data suggested that some taxonomic separations had been made on the basis of sexually dimorphic characters and ecophenotypic variation. Most intraspecific samples shared close genetic relationship, consistent with little genetic isolation. Disjunct populations of G. montereyensis and G. metzi from north of Point Conception, California, and in areas of coldwater upwelling off northern Baja California, Mexico, respectively, are very similar. The Channel Island populations are little divergent from those of the mainland, however, the San Benito Islands population is slightly more genetically distinct. Populations of the geographically isolated Guadalupe Island are genetically divergent. Patterns of genetic relationships among populations may be explained by the relatively long larval life of clinids (up to two months), geographic continuity, and major coastal current patterns. Some allelic variation in G. elegans, G. montereyensis, and G. metzi also supports longitudinal clinal trends, which may suggest selection resulting from temperature. Both allozyme and morphological data failed to separate G. erythra from G. montereyensis. Gibbonsia erythra is a deepwater ecophenotype of G. montereyensis; males inhabit deeper water than females, and the supposed distinguishing characters are sexually dimorphic and/or depth related. Gibbonsia norae is a semiisolated population of G. montereyensis inhabiting the San Benito and Guadalupe islands, Mexico. A new key to the northeastern Pacific Clinidae is given.