Minute moss beetles (Hydraenidae) are one of the most speciose and widespread families of aquatic Coleoptera, with an estimated 4,000 extant species, found in the majority of aquatic habitats from coastal rock pools to mountain streams and from the Arctic Circle to the Antarctic islands. Molecular phylogenetic works have improved our understanding of the evolutionary history of the megadiverse Hydraena, Limnebius and Ochthebius in recent years, but most genera in the family have not yet been included in any phylogenetic analyses, particularly most of those which are restricted to the Southern Hemisphere. Using a multimarker molecular matrix, sampling over 40% of described species richness and 75% of currently recognized genera, we infer a comprehensive molecular phylogeny of these predominantly Gondwanan Hydraenidae. Whilst the genera we focus on are morphologically diverse, and currently classified across all four hydraenid subfamilies, our phylogenetic analyses suggest that these Gondwanan genera may instead constitute a single clade. As a result of our findings, the African genus Oomtelecopon Perkins syn.n. is shown to nest within Coelometopon Janssens, the New Zealand Homalaena Ordish syn.n. and Podaena Ordish syn.n. are synonymised with Orchymontia Broun, and the South African Pterosthetops Perkins syn.n. is synonymised with Prosthetops Waterhouse, resulting in Pterosthetopini Perkins syn.n. being synonymised with Prosthetopini Perkins. Mesoceratops Bilton & Jäch gen.n. is erected to accommodate six former members of Mesoceration Janssens, which is shown to be polyphyletic. We propose the replacement name Orchymontia ordishi Jäch & Bilton nom.n. for Homalaena dilatata Ordish, 1984 (now a junior homonym); altogether 39new combinations are proposed. Our Bayesian divergence times infer an origin for this "Gondwana group" of genera in Africa plus Madagascar in the mid-Cretaceous and suggest that both vicariant and dispersal processes, together with extinctions, have shaped the biogeographic history of these beetles in the Southern Hemisphere during the Cretaceous, resulting in geographically conserved extant lineages. Finally, we reconstruct ancestral habitat shifts across our phylogeny, revealing numerous changes in habitat occupancy in these genera, including multiple origins of fully terrestrial, humicolous taxa in different regions.