The taxonomy of "C. nigripinnis", along with other ciscoes in the "C. artedi" complex, is unresolved. "C. nigripinnis" was recognized by W.N. Koelz in 1929 to consist of four subspecies, but he had difficulty distinguishing some specimens from "C. kiyi". The subspecies he named were "C. n. nigripinnis" in Lake Huron and Lake Michigan, "C. n. cyanopterus" in Lake Superior, "C. n. prognathus" in Lake Ontario and "C. n. regalis" in Lake Nipigon. "C. n. cyanopterus" was later synonymized with "C. zenithicus", and "C. n. prognathus" was declared a "nomen dubium". Specimens from inland lakes in central Canada are generally regarded to be "C. artedi".