Since the 1930s, eelgrass around Long Island, New York, USA, has experienced significant ecological and anthropogenic disturbances reducing areal coverage of the species. Patchiness, low density or isolation of these remaining populations increase susceptibility of this aquatic angiosperm to extinction. The loss of genetic diversity and patch connectivity, may contribute to lower fitness of eelgrass thus affecting recovery potential. Previous studies of eelgrass populations around Long Island report genetically isolated populations with low diversity. In contrast, this study found neither the evidence of inbreeding nor indications of genetic degradation for the same populations. Measures of genetic diversity such as average alleles (A = 7.59) and fixation index (F = 0.02) suggest no significant impediments to genetic connectivity among populations sampled. Gene flow (Nm = 4.58) and bottleneck analyses suggest the major disturbances of the past have not strongly affected population structure in the Long Island system. These findings have significant implications for both management and restoration. Locally, eelgrass populations in Long Island waters are unlikely to decline through genetic erosion or inbreeding processes alone. Plants from within these populations possess adequate genetic diversity to undertake restoration activities. On a larger geographic scale, the ability of these plants to maintain such high levels of genetic diversity and connectivity despite the significant areal losses historically provides optimism for the recovery potential of this species despite recent global losses.