Mexico is home to 18 species of salamanders in the family Ambystomidae. Endangered Ambystoma altamirani Dugès, 1895 is a flagship species for the Lagos de Zempoala National Park (LZNP) in central Mexico, a protected area subject to numerous anthropogenic threats. Ambystoma altamirani populations in the Park have been little studied. In 2016–2017, we surveyed four streams where populations of the species had been previously reported. Habitat variables did not differ amongst streams and three had invasive rainbow trout, but we were only able to locate one A. altamirani population in Quila, a small, cold water stream lacking fish. We captured an average of 88 individuals (total n = 354; range 53–109) across all samples in this stream, including larvae, juveniles and adults. Population estimates ranged between 53 and 127 individuals. The absence in other streams suggests reductions in the spatial extent of A. altamirani in the LZNP. We suggest rainbow trout presence in numerous streams have led to local extirpation of A. altamirani and that removal and blockage of the invasive fish and a planned re-introduction strategy might help in restoring this flagship species.