Seagrasses are important foundation species in coastal ecosystems. Genetic diversity of seagrasses can influence a number of ecological factors including, but not limited to, disturbance resistance and resilience. Seagrasses in the Indian River Lagoon (IRL), Florida are considered to be highly disturbed due to frequent events, like algal blooms, that impair water quality, reducing available light for seagrass growth. Halodule wrightii is a dominant seagrass throughout the IRL, but its genetic diversity has only been quantified in a few Gulf of Mexico and Florida Bay populations and little is known about its potential ecological consequences. I quantified the genetic variation of H. wrightii using microsatellite markers in the southern IRL to determine: (i) how disturbance history influenced genetic diversity, (ii) if morphology of clones was, in part, genetically controlled and related to disturbance history, and (iii) if genotypes showed phenotypic plasticity in response to disturbances. In the IRL, H. wrightii populations exhibited moderate genetic diversity that varied with disturbance history. The disturbance history of a population was classified by the variance in the percent occurrence of H. wrightii over a 16-year period. Genotypic richness and clonal diversity of H. wrightii increased with increasing disturbance histories. Other genetic diversity measures (e.g., allelic richness, observed heterozygosity) did not change with disturbance history. These findings suggest that impacts to seagrass coverage over time can change the genotypic composition of populations. When different genotypes of H. wrightii were grown in a common garden, differences in leaf characteristics among genotypes provided evidence that morphological trait variation is, in part, explained by genetic variance. The disturbance history of genotypes did not directly affect morphological traits. However, significant genotype x site (within disturbance history) interactions found greater variation in shoot density and below ground traits of H. wrightii genotypes from sites of intermediate disturbance history. Traits of H. wrightii were shown to be phenotypically plastic. Significant genotype x environment interactions for shoot density and height demonstrated that genotypes responded differently by increasing, decreasing, and not changing sizes in response to light reduction. Genetic diversity of H. wrightii has strong implications for ecological function in coastal communities. / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2016. / FAU Electronic Theses and Dissertations Collection