Mitocondrial DNA (mtDNA) of ciscoes from Lake Superior and seven inland lakes in Michigan and New York were analyzed for restriction fragment length polymorphism using 11 informative restriction endonucleases. Five of the 11 enzymes revealed restriction site or size polymorphism among fish. Maximum sequence divergence between mtDNA haplotypes was low (p = 0.006), indicating a maximum divergence time of 300 000 yr. Coregonus artedi and C. hoyi share mtDNA haplotype arrays indicating a more recent divergence. No unique haplotypes exist to separate C. artedi and C. hoyi from single collections, although their arrays of haplotypes are significantly different in frequencies. The lack of qualitative differentiation between C. artedi and C. hoyi noted for mtDNA parallels that previously noted for allozymes and morphology. Introgression between C. artedi and C. hoyi seems unlikely as the cause for this low amount of differentiation because a 100-base pair insertion haplotype present in Lake Superior and inland lake C. artedi is absent in C. hoyi.