Introduction of nonnative species and consequent genetic introgression of native taxa is a primary conservation concern, particularly for endangered species. Our ongoing molecular study of the endangered Sonora Tiger Salamander, Ambystoma tigrinum stebbinsi (Lowe), has uncovered evidence of introgression by the Barred Tiger Salamander, Ambystoma tigrinum mavortium. We conducted both mitochondrial DNA sequencing and analyses of nine microsatellite loci to (1) evaluate the distinctiveness of A. t. stebbinsi from the two other tiger salamander subspecies in Arizona; and (2) test for introgression in A. t. stebbinsi. Two mitochondrial haplotypes were found. One was undescribed for tiger salamanders, and the other was identical to that found in nearby A. t. mavortium. Microsatellite analyses, including assignment tests, diagnostic alleles, and high genetic distances, supported distinctness of A. t. stebbinsi. Thirty-nine animals that were putatively A. t. stebbinsi had mtDNA haplotypes identical to those in A. t. mavortium. These 39 individuals were distributed among six ponds, where a total of 73 individuals were sampled for microsatellites and considered “unknowns” because of the shared haplotype with A. t. mavortium. Assignment tests and diagnostic alleles of microsatellite data indicated that five of these 73 individuals may be hybrids of A. t. mavortium and A. t. stebbinsi. Some salamanders within the geographic range of A. t. stebbinsi were morphologically similar to A. t. mavortium or intermediate between the two subspecies. Our results suggest that introgression from introduced A. t. mavortium may be altering the gene pool of A. t. stebbinsi, thereby raising concerns about continued management of this endangered species.