RAD seq data has been generated and delivered for 70 samples of the endemic Madagascar diving beetle genus Hovahydrus (SciLife project P18862). The data will be used for phylogenomic and species delimitation analysis of the genus. The 70 samples include representatives of 3 described and 11 putative new species. Hovahydrus are excellent indicator species of pristine clear-water rainforest streams in Madagascar. The genus is likely a sister-lineage to a radiation in the Cape region in South Africa representatives of which are included as outgroups.