Genetic structure and diversity can reveal the demographic and selective forces to which populations have been exposed, elucidate genetic connections among populations, and inform conservation strategies. Beds of the clonal marine angiosperm Zostera marina L. (eelgrass) in Chesapeake Bay (Virginia, USA) display significant morphological and genetic variation; abundance has fluctuated widely in recent decades, and eelgrass conservation is a major concern, raising questions about how genetic diversity is distributed and structured within this metapopulation. This study examined the influence of bed age (<65 years versus <6 years) and size (>100 ha versus <10 ha) on morphological and genetic (allozyme) structure and diversity within Chesapeake Bay eelgrass beds. Although both morphology and genetic diversity varied significantly among individual beds (F ST ¼ 0.198), neither varied consistently with bed age or size. The Chesapeake eelgrass beds studied were significantly inbred (mean F IS ¼ 0.680 over all beds), with inbreeding in old, small beds significantly lower than in other bed types. Genetic and geographic distances within and among beds were uncorrelated, providing no clear evidence of isolation by distance at the scale of 10's of km. These results suggest that local environmental conditions have a greater influence on plant morphology than do bed age or size. They support the hypotheses that eelgrass beds are established by multiple founder genotypes but experience little gene flow thereafter, and that beds are maintained with little loss of genetic diversity for up to 65 years. Since phenotypic and genotypic variation is partitioned among beds of multiple ages and sizes, eelgrass conservation efforts should maximize preservation of diversity by minimizing losses of all beds.