RAD seq data has been generated and delivered for 95 samples of the diving beetle genus Hovahydrus from Madagascar (SciLife project P23705). The data will be used for phylogenomic and species delimitation analysis of the genus. The 95 samples include representatives of 4 described and 8 putative new species. Africophilus live in special hygropetric habitats in Madagascar, thin waterfilms on wet rock next to waterfalls or where groundwater is oozing over outcrops. The genus is a sister-lineage to remaining Laccophilini and restricted to the Afrotropical region. It is a very old lineage.