Molecular genetic methods were used to quantify natural hybridization between rainbow trout Oncorhynchus mykiss or steelhead (anadromous rainbow trout) and coastal cutthroat trout O. clarkii clarkii collected in the Copper River delta, Southeast Alaska. Eleven locations were sampled to determine the extent of hybridization and the distribution of hybrids. Four diagnostic nuclear microsatellite loci and four species-specific simple sequence repeat markers were used in combination with restriction fragment length polymorphism analyses of NADH dehydrogenase 5/6 (ND5/6) mitochondrial DNA (mtDNA) to investigate the genetic structure of trout from both species and identify putative interspecific hybrids. Hybrids were found in 7 of the 11 streams sampled in the Copper River delta, the extent of hybridization across all streams varying from 0% to 58%. Hybrid trout distribution appeared to be nonrandom, most individuals of mixed taxonomic ancestry being detected in streams containing rainbow trout rather than in streams containing coastal cutthroat trout. Genotypic disequilibrium was observed among microsatellite loci in populations with high levels of hybridization. We found no significant correlation between unique stream channel process groups and the number of hybrid fish sampled. Eighty-eight percent of fish identified as first-generation hybrids (F₁) in two populations contained coastal cutthroat trout mtDNA, suggesting directionality in hybridization. However, dominance of coastal cutthroat trout mtDNA was not observed at a third location containing F₁ hybrids, indicating that interspecific mating behavior varied among locations. Backcrossed individuals were found in drainages lacking F₁ hybrids and in populations previously thought to contain a single species. The extent and distribution of backcrossed individuals suggested that at least some hybrids are reproductively viable and backcrossed hybrid offspring move throughout the system.