The largest diversity in the world of subterranean diving beetles (Dytiscidae) has been discovered in underground waters of the Australian arid zone. The majority of species are from the Dytiscidae genera Limbodessus Guignot, 1939 (Bidessini) and Paroster Sharp, 1882 (Hydroporini) and are distributed within two major regions: calcrete islands of central Western Australia and the Ngalia Basin of the Northern Territory. Here, we use an integrative approach based on morphological and molecular analyses to describe Ngaliadessus humphreysi gen. et sp. nov. Watts & Villastrigo representing a new genus and species of stygobiotic Bidessini collected from a single well in the Ngalia Basin. Phylogenetic analyses using whole mitochondrial genome, Histone 3 and 18S rRNA data, representing a comprehensive coverage of Bidessini genera, support the distinction of the genus and species as a separate evolutionary lineage sister to the Australasian genus Limbodessus and the widely distributed genus Allodessus Guignot, 1953. Our study further confirms that the Ngalia Basin, containing 13 subterranean dytiscid species from four distinct genera, is one of the most speciose areas within the world's most diverse hotspot of subterranean diving beetles.