Round goby (Neogobius melanostomus) is an invasive fish present in all five Great Lakes and is becoming increasingly common in their tributaries. Johnny darter (Etheostoma nigrum) is a native species that often coexists with N. melanostomus. In this work, historic factors are addressed as a source of genomic variation in study populations of these species. To do this, patterns of variation in the mitochondrial gene NADH dehydrogenase subunit 2 (ND2) were characterized for both species throughout Lower Michigan. Populations of N. melanostomus and E. nigrum were sampled from 17 localities representing both eastern and western basins of Lower Michigan to test the hypothesis that populations differ between the eastern and western basins of the Great Lakes. Neogobius melanostomus populations were largely homogenous with no significant differences detected among populations or between the eastern and western basins. Additionally, N. melanostomus exhibited no evidence of overarching historical genetic structure, consistent with the recent invasion and rapid expansion of this species. Etheostoma nigrum exhibited significant differentiation among local populations; however, similarity among mtDNA haplotypes indicated that differences among populations are recent, suggesting that local forces are a more important factor in shaping patterns of variation than historical factors. Contrary to predictions, there were no significant differences detected between the eastern and western basins of the Great Lakes; however, construction of a neighbor joining tree with F_st estimates revealed clustering of populations by basin with some anomalies. These anomalies may be the result of recent stream capture events facilitating gene flow between the two basins.