We used two mitochondrial and eight nuclear microsatellite gene loci to compare genetic diversity and genetic affinities of white suckers (Catostomus commersonii) introduced into the Rio Grande of northern New Mexico to putative source populations in the Pecos and Canadian rivers of northeastern New Mexico. Estimates of genetic diversity based on allelic identity were similar among localities from all three drainages, whereas samples of non-native white suckers from the Rio Grande exhibited greater genealogical diversity. We attributed increased genetic diversity in the Rio Grande to separate introductions from ≥2 genetically distinct source populations, only one of which appeared to be from either the Pecos River or the Canadian River. There also was a divergent haplotype in the Pecos River, consistent with the introduction of a non-native lineage into this native population.