Like many imperiled fishes, the endangered Pahrump Poolfish (Empetrichthys latos latos) is managed in ex situ refuges. I investigated life history characteristics of females from two such populations at Lake Harriet and Shoshone Stock Pond. Lake Harriet is a relatively large lake with low fish densities located at relatively low elevation and low latitude, while Shoshone Stock is a small pond with high fish densities at a higher elevation and latitude. Females from the Lake Harriet population were larger, and had greater fat content, reproductive allocation, and ‘clutch’ size than females from the Shoshone Pond population. This divergence, which occurred in three decades, may result in a phenotypic mismatch if the fish are used as a source for restocking their native habitat or stocking new refuges. Poolfish conservation may require establishing new populations; however, many sites are inhabited by non-native fish and/or other protected fish species. Thus, managers may wish to consider establishing multi-species refuges that may even already include undesirable species. I established experimental communities that included allopatric and sympatric communities of Poolfish, Amargosa Pupfish (Cyprinodon nevadensis), and invasive Western Mosquitofish (Gambusia affinis). Pupfish persisted in sympatry with both poolfish and mosquitofish, but had higher juvenile production when maintained in allopatry. By contrast, poolfish juvenile production was high in allopatry, but virtually absent in the presence of other species. To evaluate the generality of these findings, I established experimental allopatric and sympatric communities of poolfish or pupfish with mosquitofish from two populations that differed in body size: Garrett mosquitofish were approximately twice the mass of Wabuska mosquitofish. Poolfish juveniles had high survival in allopatry, but produced virtually no juveniles when sympatric with either of the two mosquitofish populations. Pupfish juvenile survival was higher in allopatry than sympatric with Garrett mosquitofish, which in turn was higher than sympatric with Wabuska mosquitofish. These results were consistent with the earlier experiment suggesting that poolfish were functionally extirpated but pupfish maintained substantial production in the presence of mosquitofish. These findings suggest that poolfish should be maintained in single species refuges, but that multi-species refuges may protect imperiled pupfish species.