The distribution and ecology of fishes in 457 sampling sites on 175 streams of the San Francisco Bay drainage, California, was determined between 11 May and 10 October 1981. Of 35 species collected, 22 (63 percent) were exotic to California and 13 (37 percent) were native. Urbanization has resulted in the alternation and destruction of many stream habitats within the basin, and in changes in the dominance of fish assemblages from native to introduced species. Four native species, Rhinichthys osculus, Eucyclogobius newberryi, Pogonichthys macrolepidotus, and Gila crassicauda, are apparently extinct in study area streams in which they historically occurred. Several other species, Oncorhynchus kisutch, Mylopharodon conocephalus, Hysterocarpus traskii, and Archoplites interruptus, have experienced significant reductions in their ranges. The abundance of native fishes was positively correlated with the occurrence of other native species primarily in stream habitats with little noticeable human disturbance. The abundance of introduced fishes shows a significant negative correlation with the occurrence of native species. Introduced fishes occurred primarily in large, highly disturbed pools at low and intermediate elevations, often in channelized stream sections. Local extinctions of isolated populations of native fishes throughout the basin will continue to occur should aquatic habitat alteration continue at its present rate.