MtDNA diversity in contemporary samples from eight populations of walleye from eastern Lake Huron was negatively associated with the relative amounts of anthropogenic impacts experienced by each. MtDNA diversity was also compared in contemporary and archival samples from two populations. In one instance, contemporary samples had reduced mtDNA diversity compared to archival samples collected before major exploitation. No such difference was detected between contemporary and archival samples from the second population where commercial exploitation and habitat alteration have been more limited. Low mtDNA diversity in artificially produced fish relative to parental sources suggests that culture programmes might be one mechanism lowering mtDNA diversity in populations. A phylogenetic comparison of walleye mtDNA haplotypes revealed that an analysis based on restriction fragment length polymorphisms in two amplified fragments surveyed 554bp and detected almost twice the number of mutations and haplotypes than did a sequence analysis of 513nt of the control region.