After an estimated five million years of independent evolution, the barred tiger salamander (Ambystoma tigrinum mavortium) was introduced by bait dealers into the native range of the California tiger salamander (A. californiense). Hybridization and backcrossing have been occurring in central California for 50–60 years, or an estimated 15–30 generations. We studied genetic and ecological factors influencing admixture of these two divergent gene pools by analyzing frequencies of hybrid genotypes in three kinds of breeding habitats: natural vernal pools, ephemeral man-made cattle ponds, and perennial man-made ponds. Perennial ponds tended to have higher frequencies of nonnative alleles than either type of seasonal pond, even in cases where perennial and seasonal ponds are within a few hundred meters. Thus, the hybrid zone has a mosaic structure that depends on pond hydrology or ecology. The presence of some broadly acting constraints on admixture is suggested by linkage disequilibria between physically unlinked molecular markers within ponds. In addition, we found several marker-specific deviations from Hardy-Weinberg equilibrium. One marker showed a consistent deficit of heterozygotes across pond types. Another showed heterozygote deficits only in vernal pools. A third was more likely to have heterozygote excess in ephemeral cattle ponds. These patterns indicate that admixture is influenced by complex genotype-by-environment interactions.