It is endemic to the Pecos River watershed in eastern New Mexico and western Texas in the United States.

Despite once existing throughout the Pecos River, C. pecosensis populations have become increasingly isolated due to significant portions of their native habitat being removed.

[2][3] Following the introduction of Cyprinodon variegatus (sheepshead minnow), pure Pecos pupfish populations have been further isolated and largely exist in scattered sinkholes, man-made impoundments, and marshes.

[6][7] The widespread success of hybrids, and quick range expansion throughout native Pecos pupfish waters, has been hypothesized to be the result of selection mechanisms for hybrids during a period when the native C. pecosensis population had experienced a reduction.

[8] Additionally, hybrid populations have been reported to have increased growth-rates and vigor (Heterosis), resulting in Pecos pupfish females to actively choose to mate with hybrids over pure male Pecos pupfish.