We examined the genetic population structure of Spartina alterniflora in Jamaica Bay, Queens, NY and the surrounding area in order to assist the ongoing restoration of Jamaica Bay. AMOVA (Analysis of Molecular Variance) indicated that population differences accounted for 15% of molecular variance (Φ PT = 0.15, p = 0.001). Observed heterozygosity (Ho) ranged from 0.61 to 0.73 among populations. A Mantel test indicated a weak and non-significant correlation between pairwise Φ PT and geographic distance matrices (r = 0.34, p = 0.12). A PCA revealed no obvious grouping pattern for sampled populations. Based on these data, we determined that the studied populations contained similar genetic variability to other populations in the New York vicinity and to those of the entire region. It seems likely that collection of germplasm from within the region will prove sufficient in maintaining overall genetic variation in restoration plantings. Given the small amount of genetic structure among populations within Jamaica Bay, however, it would be prudent to collect widely within the target marsh. We also recommend the practice of propagating plugs of S. alterniflora from wild seed, as opposed to using vegetative cuttings, when creating planting stock, in order to maximize genetic diversity in restored marshes.