Alnus maritima (Marsh.) Muhl. ex Nutt. is a rare woody plant species that exists as three subspecies found in widely disjunct locations in the United States. Although there is a growing interest in the phytogeography, ecology, conservation, and landscape potential of this species, the phylogeny of A. maritima has not yet been resolved by using molecular methods. We have combined a relatively new method of genome fingerprinting, ISSR-PCR, and the automated imaging capabilities of GeneScan technology to investigate the molecular systematics of A. maritima. Based on the molecular evidence from 108 ISSR loci, we confirm that the three disjunct populations of A. maritima have diverged sufficiently to be classified as subspecies. Our molecular phylogeny of the three subspecies of A. maritima agreed in topology with a phylogeny produced from morphological data and showed that subsp. oklahomensis is the most distinct of the three subspecies and was the first to diverge. The simultaneous analysis of molecular and morphological data provides a detailed and balanced phylogeny reconstruction for the three subspecies. Our results support the theory that A. maritima originated in Asia, migrated into North America across the Bering land bridge, and was established over a large range in the New World before being forced into its present meager disjunct distribution.