The genetic diversity of peripheral populations is potentially important to the future adaptive capacity of species, although may be difficult to predict. A large number of species-at-risk in Canada are at the northern edge of their distribution, and many of these live in fragmented habitat. We used nuclear and chloroplast markers to assess patterns of genetic diversity and differentiation within and among populations of Canadian Magnolia acuminata (Cucumber tree), an endangered species in Canada that extends as far north as the fragmented Carolinian forest in southern Ontario. We also compared the genetic composition of Canadian M. acuminata to populations sampled throughout its central distribution in the USA. We found a high proportion of shared microsatellite alleles, plus a single cpDNA haplotype, distributed throughout the entire M. acuminata range. We also found that despite occupying fragmented habitat at their range periphery, Canadian populations showed little reduction in genetic diversity relative to the USA populations, and we attribute this to effective historical dispersal in a longlived, polyploid species. However, a combination of private alleles, genetic substructuring, and lower levels of genetic diversity in seedlings compared to mature trees, suggests that current levels of gene flow are relatively low among Canadian populations. Therefore, despite high levels of genetic diversity in Canadian M. acuminata, managers should be aware that without intervention, populations will likely become increasingly isolated and experience a reduction in genetic diversity which in turn may threaten their long-term survival in Canada.