AbstractHybrid zones represent natural laboratories to study gene flow, divergence and the nature of species boundaries between closely related taxa. We evaluated the level and extent of hybridization betweenCrocodylus moreletiiandCrocodylus acutususing genetic and morphological data on 300 crocodiles from 65 localities. To our knowledge, this is the first genetic study that includes the entire historic range and sympatric zone of the two species. Contrary to expectations, Bayesian admixture proportions and maximum‐likelihood estimates of hybrid indexes revealed that most sampled crocodiles were admixed and that the hybrid zone is geographically extensive, extending well beyond their historical region of sympatry. We identified a few geographically isolated, nonadmixed populations of both parental species. Hybrids do not appear to be F1s or recent backcrosses, but rather are more likely later‐generation hybrids, suggesting that hybridization has been going on for several to many generations and is mostly the result of natural processes.Crocodylus moreletiiis not the sister species ofC. acutus, suggesting that the hybrid zone formed from secondary contact rather than primary divergence. Nonadmixed individuals from the two species were distinguishable based on morphological characters, whereas hybrids had a complex mosaic of morphological characters that hinders identification in the wild. Very few nonadmixedC. acutusandC. moreletiipopulations exist in the wild. Consequently, the last nonadmixedC. moreletiipopulations have become critically endangered. Indeed, not only the parental species but also the naturally occurring hybrids should be considered for their potential conservation value.