Genomics, transcriptomics, and proteomics are rapidly increasing our knowledge of non-model species biology, and is increasingly being used to benefit conservation initiatives for threatened species. Here, we generated whole genome sequence data for a male smalltooth sawfish, which is an endangered elasmobranch. Genetic datasets for this highly threatened species will facilitate the development of molecular tools to improve knowledge of its biology and ecology, ultimately allowing the implementation of informed management strategies.