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We studied patterns of allozymic variation among wild and captive populations of endangered desert pupfish Cyprinodon m. macularius. Much of the existing variation can be attributed to different founder sources,founder and bottleneck effects, or a combination of all three. Local isolation, either natural or artificial, promotes divergence of both wild and captive populations. Divergence was countered over the natural long-term condition of drought by dispersal and population mixing during brief wetter periods. Such gene flow among populations is now precluded by anthropogenic control of hydrologic pattern. Recovery of this species to self-sufficiency will likely require re-establishment of a natural hydrology, which, for the foreseeable future, is unlikely in the lower Colorado River basin. If this charismatic desert species is to survive, resource managers must combine knowledge of ecological and genetic patterns with political realities. Until natural habitats are re-established, a captive management program that more closely mimics patterns of alternating gene flow and isolation should be implemented. (C) 1998 Elsevier Science Ltd. All rights reserved.