Water mites of the Brachypodopsis baumi species complex are confined to SE Asia, and up to now have been considered to belong to one species only. In the present study we used morphological data and DNA barcoding (556 bp of the mitochondrial gene cytochrome c oxidase subunit I, COI) to resolve taxonomic issues within the species complex from Borneo. The use of an integrative-taxonomy approach confirmed the identification of two “cryptic” species., i.e., Brachypodopsis crockerensis sp. nov. and B. kinabaluensis sp. nov. and one “pseudocryptic” species B. selampandei sp. nov. Based on phylogenetic analyses, Paraxanopsis truncata was transferred to the subgenus Brachypodopsis (s. s.). Brachypodopsis. gibberipalpis (Viets, 1935), a taxon previously synonymized with B. baumi, which is reinstated as a valid species.