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Using data from eight autosomal microsatellite loci, we investigated levels of within- and between-site variation in the seagrass Zostera marina L. (eelgrass) from eight locations in the San Juan Archipelago, located in the northwest corner of Washington, USA. Only 117 of the 365 samples collected were unique individuals, and there were large differences in the estimates of clonality among sites. Site-specific genotypic richness ranged from 0.082 to 0.688, and the distribution of ramets and genets varied widely within sites. No multilocus genotypes were shared between sites. We found significant differences in distribution of alleles and variance in allele frequencies among sites, suggesting substantial genetic population substructuring. We detected low levels of genetic diversity in two sites known to have undergone recent declines and a genetic signature of population expansion in a site known to be increasing. Thus, like elsewhere, we find that genetic studies add an important component to monitoring programs in this region.