The importance of exogenous selection in a natural hybrid zone between the pupfishes Cyprinodon atrorus and C. bifasciatus was tested via spatio-temporal analyses of environmental and genetic change over winter, spring, and summer for three consecutive years. A critical influence of exogenous selection on hybrid zone regulation was demonstrated by a significant relationship between environmental (salinity and temperature) and genetic (three diagnostic nuDNA loci) variation over space and time (seasons) in the Rio Churince system, Cuatro Ciénegas, Mexico. At sites environmentally more similar to parental habitats, the genetic composition of hybrids was stable and similar to the resident parental species, whereas complex admixtures of parental and hybrid genotypic classes characterized intermediate environments, as did the greatest change in allelic and genotypic frequencies across seasons. Within hybrids across the entire Rio Churince system, seasonal changes in allelic and genotypic frequencies were consistent with results from previous reciprocal transplant experiments, which showed C. bifasciatus to suffer high mortality (75%) when exposed to the habitat of C. atrorus in winter (extreme temperature lows and variability) and summer (abrupt salinity change and extreme temperature lows and variability). Though unconfirmed, the distributional limits of C. atrorus and C. atrorus-like hybrids appear to be governed by similar constraints (predation or competition). A crucial link was also established between contemporary exogenous selection in a hybrid zone between these species and previous demonstration of long-term evolutionary significance of environmental variation and introgression on the phenotypic diversification Cuatro Ciénegas Cyprinodon.