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Twelve species of pupfish (Genus Cyprinodon) generally are recognized in the northern Chihuahuan Desert. Eight of these are restricted to relatively small spring systems, whereas the remaining four occur in springs and riverine situations. The present abundance and distribution of pupfishes in the region is only a remnant of what must have been present prior to anthropogenic watershed deterioration and depletion of groundwater. Today, most spring-dwelling pupfishes are succumbing to losses of springflows, primarily as a result of pumping of groundwater, and the riverine species are adversely affected by a diversity of anthropogenic factors. The diversity of both groups has declined as a result of introgressive hybridization with a non-native pupfish, the wide ranging coastal species C. variegatus. The rapidity with which native stocks can be lost as a result of such hybridization is dramatically illustrated by events following the introduction of C. variegatus into the Pecos River Basin in the 1960s. A similar threat is posed by transport of any non-native pupfish into waters occupied by an endemic pupfish.