We used protein electrophoresis to study the distribution of hybrids between Pecos pupfishCyprinodon pecosensisand introduced sheepshead minnowC. variegatusin the Pecos River, New Mexico–Texas. Pecos pupfish populations in New Mexico apparently are free of hybrid influence except in waters near the New Mexico–Texas state boundary. In Texas, hybrids have replaced Pecos pupfish throughout 430 km of the Pecos River and have spread into downstream areas well outside the recorded range of Pecos pupfish. Hybrids are nearly ubiquitous in waters peripheral to the river, occurring in irrigation canals, reservoirs, and water-filled, commercial gravel pits. Unintrogressed Texas populations of Pecos pupfish occur only in a small tributary of the Pecos River and in a large gravel pit. Similarities in the genetic structure of hybrid pupfish populations in the Pecos River and peripheral waters suggest that the spread of alleles characteristic of sheepshead minnow has been accomplished by dispersal of hybrids, rather than by multiple introductions of sheepshead minnow.