Loss of genetic diversity and isolation of populations present threats to rare species. These threats can be compounded by using small stocks to establish new populations; however, such restoration efforts are essential to buffer species against stochastic effects. Genetic markers can be used in restoration to assure sufficient genetic diversity to prevent inbreeding depression; minimize outbreeding depression, which can result from introductions using multiple differentiated stocks; establish the origin of extant populations, which permits populations to be reestablished using local stocks; and monitor newly established populations for interbreeding or success of different stocks. We used genetic markers to study the effects of establishing new populations of a rare California endemic fish, Sacramento perch (Archoplites interruptus; family Centrarchidae), and to make recommendations for establishing new populations of this species from stocks. Perch are important to the restoration of California's Central Valley ecosystems because they are a top aquatic predator. However, the species is vulnerable because the only remaining populations are outside its native range (due to human translocations). We evaluated genetic diversity in eight recently established populations of perch using 12 microsatellite DNA loci. We discovered that six of the eight populations experienced genetic bottlenecks and genetic drift, resulting in significant differentiation among populations. Additionally, we sequenced 350 base pairs of the mitochondrial control region from bone and formalin preserved samples from extirpated populations, which allowed us to determine that the species originally had substantial metapopulation structure. This structure allowed us to infer the origin of one of the extant populations.