SRP373774 PRJNA835347 De novo assembly and annotation of the transcriptome of the regionally endangered seagrass Zostera capensis Due to its declining fragmented populations and sensitivity to anthropogenic impacts, the dominant seagrass in South Africa, Zostera capensis Setchell, is listed as vulnerable on the IUCN Red List. Anthropogenically forced climate change is projected to increase the incidence of climatic extremes. Addressing questions about how these climatic extremes will affect foundational species such as Z. capensis and how to restore the declining populations requires investigations of functional responses within and between populations along its distribution. Ecological transcriptomics would be a useful approach for studying functional responses of Z. capensis through quantification of gene expression changes in response to environmental changes. Here, we present the first reference transcriptome of Z. capensis libraries sequenced on the Ion Torrent S5 platform