Two questions relevant to the management of species threatened by introgressive hybridization are whether results from different genetic marker are comparable, and whether all sources of introgression have been identified. We used recently-developed SNP markers to quantify introgression from two non-native taxa: rainbow trout (Oncorhynchus mykiss) and cutthroat trout of the Yellowstone evolutionary lineage (O. clarkii subspp.), into populations of threatened Lahontan cutthroat trout (O. c. henshawi). Results for O. mykiss introgression largely agreed with those of previous studies using different genetic markers. However, three populations contained much genetic material from the Yellowstone lineage, a source of introgression not previously examined. This included one population proposed to be a remnant of an extinct cutthroat trout lineage.