Novel populations pose unusual challenges for wildlife managers because knowledge regarding the source of these populations is essential to develop sound management approaches. One example that illustrates the complexity of this issue is the small population of red squirrels (Tamiasciurus hudsonicus) identified in northeastern Illinois in the 1970s. To elucidate the source of the red squirrel population in Illinois, we examined both contemporary and less recent patterns of genetic structure using nuclear microsatellite loci and mitochondrial DNA. Analyses revealed the Illinois subpopulation was primarily comprised of descendents of immigrants from Indiana, but there was also evidence of a translocation of squirrels from Minnesota. We recommend continued protection for the red squirrel in Illinois due to its restricted geographic range, small population size, and status as a native population.