The dominant species of seagrass in NY, Zostera marina, has experienced several historical die-offs and is currently under heavy stress due to water quality and other anthropogenic problems. The consequences of these events on the genetic diversity and population structure of the remaining grass beds are unknown. This thesis addresses questions regarding the genetic diversity of extant populations, and how this information can aid current conservation and restoration efforts. Plant morphometrics and genetic samples of Zostera marina were collected at sites across Great South Bay, Shinnecock Bay, Peconic Bay and the Long Island Sound. Each individual was genotyped at 8 different microsatellite loci. Analysis of microsatellite alleles was used to examine the genetic diversity, population structure and gene flow between meadows within and between bays. Moderate levels of clonal and genetic diversity were exhibited across all study areas. No evidence of local inbreeding or of a severe population bottleneck was found. With the exception of individuals sampled from around Fishers Island in the Long Island Sound, connectivity is high within and between the major Long Island estuaries examined in this thesis. These results suggest the existence of an abundance of potential donor material from Great South Bay, Shinnecock Bay and the Peconics suitable for transplant within or between any of the three bays based on genetic criteria. However, continued monitoring of genetic diversity and additional documentation and small-scale sampling of future restoration efforts is important in maintaining current levels of genetic diversity.