A key element in understanding hybridization in fishes is to determine the relative influences of endogenous and exogenous selection on hybrid zone structure. To date, such studies have been limited. To help fill this gap, we conducted reciprocal transplant experiments with two pupfish species, Cyprinodon atrorus and C. bifasciatus, to assess the importance of environmental factors in their hybridization dynamics. Results from our experiments show that C. atrorus survives well when environmental variability is low or high, whereas C. bifasciatus only survives well when environmental variability is low. This corroborates the hypothesis that C. atrorus is euryplastic and C. bifasciatus stenoplastic, and also provides evidence that differential environmental tolerance may be important in regulating the distribution of genetic variation in hybrid zones between these species. However, these differences do not explain why C. atrorus is absent from C. bifasciatus habitats. This absence is likely determined at least in part by other exogenous selection factors, such as disproportionate predator susceptibility and/or inferior competitive ability of C. atrorus. Although the relative role of endogenous selection in this system remains unknown, this study provides insight into the potential complexity of exogenous selection in fish hybrid zones.