Salt marshes are ecologically and economically valuable ecosystems in worldwide decline, and are dominated in the southeastern United States by the clonal macrophyte black needlerush (Juncus roemerianus Scheele). Clonal and genetic diversity of foundational plant species in monotypic ecosystems, such as the salt marsh, are important for ecosystem processes and resiliency, especially under impending sea level rise and climate change. Gene flow, dependent on population connectivity, maintains genetic diversity in highly fragmented populations and can be affected by anthropogenic land conversion typical of coastal areas. However, no genetic studies have been conducted on J. roemerianus despite the species' importance to the salt marsh as a dominant, foundational plant species. We used next-generation sequencing to develop a panel of 19 species-specific microsatellite markers for use in population and landscape genetic studies on J. roemerianus. A study on 304 samples from a large, natural population of J. roemerianus within the Grand Bay National Estuarine Research Reserve, MS found higher than expected clonal and genetic diversity for a species assumed to have rare sexual reproduction. Patterns of clonal and genetic diversity and population structure were examined in a population genetic study using 849 samples collected at seventeen sites across a significant portion of the species' range from Mississippi to South Carolina. Clonal and genetic diversity was higher than expected with an average genotypic diversity of 0.67 and average observed heterozygosity of 0.56. Differences in diversity measures across the Gulf and Atlantic coast suggest environmental influences on life history and possible local adaptation. Broad scale structure with samples grouping into three genetic clusters indicated gene flow might be more frequent than suggested by life history literature. A landscape genetic analysis using hierarchical model selection across a least cost transect analysis was performed across 576 samples collected at ten sites in the northeastern Gulf of Mexico to determine the influence of landscape features on population connectivity. Coastal corridors were identified as important for J. roemerianus dispersal, and coastal development negatively influenced population connectivity. Results critically contribute to ecological and evolutionary knowledge on J. roemerianus, and have important implications for coastal conservation, restoration, and management.