Zostera capensis is a keystone species providing essential ecosystem services to southern African coastal systems. Like most seagrasses globally, Z. capensis is declining and under threat from anthropogenic pressures, and indicators of seagrass health and resilience may be of interest in preventing further declines. As intraspecific diversity is an important component of resilience, we used a pooled RADseq approach to generate genome-wide measures of variation across the entire South African distribution of Z. capensis. Using nucleotide diversity, heterozygosity and allelic richness we tested for associations with fine-scale anthropogenic pressure data compiled by the South African National Biodiversity Assessment using generalised linear models. Increased fishing effort, habitat loss, sand mining and a change in estuary flow dynamics were found to play an important role in decreasing nucleotide diversity and expected heterozygosity, most likely due to the loss of less resilient genotypes as a result of direct physical damage or indirect consequences. As the building block for adaptation, nucleotide diversity is particularly important for resilience. Because of this, as well as the fact that nucleotide diversity displayed the most distinct difference between the west and east coast, and responded most strongly to anthropogenic pressures, we suggest that this may be a useful measure for monitoring genetic or genomic variation. As genomic diversity influences resilience and resistance to disturbances, the remaining diversity in South African seagrass beds urgently needs to be conserved through restoration efforts and careful management of pressures.