<p>Seagrass production is threatened by multiple stressors that are increasing as a consequence of global climate change. Seagrass beds could be more productive if they are genetically diverse, with traits adapted to an array of abiotic conditions, and if beds maintain genetic variation through gene flow. <i>Halodule wrightii</i> is a seagrass used in restoration and forms critical habitat in the northern Gulf of Mexico, where there is high abiotic variation. In this setting, for <i>H. wrightii</i> beds, it was hypothesized that genetic diversity would be positively correlated to trait variation and that beds experiencing high abiotic stress (elevated temperatures and low salinities) would have low production and diminished genetic diversity from selection. Because of negatively buoyant seeds and abiotic variation, it was hypothesized that gene flow between beds would be rare. Seven beds located within four bays were visited. These beds span from west (Grand Bay, Mississippi) to east (Apalachicola Bay, Florida) and subsequently differ in distance from freshwater influence of the Mississippi River. At each bed, leaves for microsatellite genotyping were collected, plant morphological traits were measured, and temperature and salinity were continuously recorded. Western sites had lower mean salinity, greater duration below 10 psu, and lower belowground biomass than eastern sites. Genotypic richness was spatially variable and was not related to production nor traits. Beds exhibited isolation by distance and environment. Genetic differentiation (<i>F</i>_ST) was attributed to temperature range, which coincided with a west-to-east directionality of bays. Managers should consider isolation patterns in combination with abiotic extremes when determining conservation actions.</p>