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The Northern Sunfish (Lepomis peltastes Cope, 1870) is threatened in New York state, USA, but this was not the case before 1940 when the NY Biological Survey documented the species at scattered, specialized habitats in six watersheds in the central and western parts of the state. After 1940 the historic populations could not be detected, but a new population was discovered in 1974 in lower Tonawanda Creek and the nearby Erie Canal. Northern Sunfish, and a few of their hybrids with other Lepomis species, were caught at these locations during irregular sampling through 2009, but no Northern Sunfish were caught after 2009. The objectives of our study were to: (1) Determine the extent of Northern Sunfish hybridization with other Lepomis species, and (2) Evaluate how well identifications of Lepomis species and their hybrids agreed among field keys, morphometric measurements and meristic counts, and genetic methods. In 2013, we collected Northern Sunfish (descended from fish captured in lower Tonawanda Creek from 2006-2009) from NY State Department of Environmental Conservation rearing ponds, plus wild Green Sunfish (L. cyanellus Rafinesque, 1819), Pumpkinseed (L. gibbosus Linnaeus, 1758), Bluegill (L. macrochirus Rafinesque, 1819), and suspected Lepomis hybrids from lower Tonawanda Creek. Ultimately, 91 fish were identified using field keys, morphometric-meristic analysis, and mtDNA and nuclear DNA analysis. Assuming genetic analysis provided accurate identification, we found 7 Bluegill × Northern Sunfish, 8 Bluegill × Pumpkinseed, 13 Bluegill × Green Sunfish, and 3 Green Sunfish × Pumpkinseed hybrids in our sample (female parent listed second in these crosses). Keyed and morphometric-meristic identifications did not differ in accuracy and averaged 81% of genetic identification accuracy. After Northern Sunfish stocking (not in our study area) and sampling from 2008 to 2018 in several watersheds with appropriate habitat and no recaptures after 2014, we conclude that the Northern Sunfish is extirpated in western New York state.