The Beaver Island group in Lake Michigan comprises nine islands ranging from 0.3 to 144 km2, lying approximately 30 km west of Michigan’s Lower Peninsula (LP) and 15 km south of the Upper Peninsula (UP). The islands have been isolated from mainland Michigan for most of their postglacial history, but were connected to the mainland LP during the low-water Chippewa stage (ending about 7400 years before present (YBP)). Although plants and animals could have colonized the islands during the Chippewa period, flooding during the subsequent Nipissing high-water stand means that the smaller islands have been colonized more recently. We analyzed 481 bp of mitochondrial D-loop sequences from woodland deer mice (Peromyscus maniculatus (Wagner, 1845)) on six of these islands in northern Lake Michigan to elucidate the mainland origin and minimum number of colonization events for this species. Surprisingly, the distribution of haplotypes on the islands suggests that the populations on most islands likely had separate recent origins on the mainland UP. Approximate Bayesian computation supports a scenario in which individual islands were colonized separately by distinct groups of mice. Together, the data suggest multiple colonization events from the UP, rather than expansion from a bottlenecked population or a single colonization event.