Two species of smelt (Osmeridae), Hypomesus transpacificus and Spirinchus thaleichthys, found in the Sacramento-San Joaquin estuary recently have declined in abundance, and H. transpacificus has been threatened by the introduction of nonnative Hypomesus nipponensis. We conducted an allozyme analysis of five species of smelt found in California to determine whether the threatened populations are distinct genetically and to evaluate the possibility of introgression of foreign alleles in H. transpacificus. Native H. transpacificus and introduced H. nipponensis differed genetically (Nei's D = 0.883) and were allelically distinct at 13 of 22 loci. Hypomesus transpacificus is more similar genetically to the native marine species, Hypomesus pretiosus (Nei's D = 0.400) than to H. nipponensis, strongly supporting the interpretation that H. transpacificus and H. nipponensis are distinct species. Populations of S. thaleichthys from Washington and the Sacramento-San Joaquin delta are similar genetically (Nei's D = 0.005). However, gene frequencies among these two populations of S. thaleichthys differed significantly, suggesting that current gene flow between them is restricted. This result, combined with geographic isolation suggests that the delta population of S. thaleichthys warrants management as an isolated and genetically distinct entity.