Effective conservation requires an understanding of the genetic interactions among populations and individuals of a species, particularly those with fragmented, isolated distributions. Alnus maritima (seaside alder) is a rare tree species with an extremely fragmented distribution of highly isolated populations in the Delmarva Peninsula, Georgia, and Oklahoma. We conducted a mating system study to estimate the outcrossing rate, inbreeding coefficient, biparental inbreeding rate, and correlation of paternity in progeny from a Georgia and an Oklahoma population to investigate the effects of isolation on the A. maritima mating system. Data from nine microsatellite loci showed similarly high multilocus outcrossing rates in both populations (t_m  =  0.94). Individual tree outcrossing rates were also high (t_m  =  0.873–1.047). There was no significant biparental inbreeding in either population, but there was significantly higher correlated paternity in the Oklahoma population. Results showed the high outcrossing expected for a wind-pollinated, monoecious species that can promote the maintenance of genetic variation detected in A. maritima seed pools and standing populations. Likewise, pollen flow among Oklahoma populations may promote maintenance of regional genetic variation. However, despite the genetic diversity in the seed pool generated by A. maritima's highly outcrossed mating system, failure of new individuals to be recruited into populations from seed presents an obstacle that will need to be considered when developing conservation strategies for this rare species.