In 1985 and 1986 we sampled streams of the San Joaquin River drainage in south-central California. The purposes of the survey were: (i) to see if further declines in native fish populations had occurred since 1970 when they were last surveyed; (ii) to verify the species distributions and species-habitat relationships observed in previous studies; (iii) to verify the species assemblages observed in previous studies; and (iv) to determine the status of the recently described Kern brook lamprey (Lampetra hubbsi). We also reviewed the status of the native fish fauna as compared to pre-European times. Only 11 species of the original fauna of 19 species were found and only 6 of the 11 were common. Hardhead (Mylopharodon conocephalus) and hitch (Lavinia exilicauda) were found in fewer localities than in 1970. The decline in hardhead was associated with an expansion of smallmouth bass (Micropterus dolomieu) populations. Three assemblages of native species were identified, in agreement with earlier studies. A fourth assemblage identified in earlier studies, composed largely of introduced fishes, was divided into two subgroups on the basis of our analysis. Each assemblage of species was associated with a distinct set of habitat characteristics. Populations of Kern brook lamprey were found in the Kaweah, Kings, San Joaquin, and Merced rivers. Lampreys were absent from the lower reaches of the rivers and, except in the Kings River, were only found below major dams. In the Kings River lampreys were captured above and below Pine Flat Reservoir. Because the populations are restricted in range, effectively isolated from one another, and all but one can be affected by reservoir operations, special protection for them is warranted.