We review morphology and systematics of Phoxophrys using new specimens of previously rare species. In addition to external characters, we relied heavily on skull morphology visualized using computed tomography data of all currently recognized species in this genus. Phylogenetic analysis of ND4, 12S, and 16S mDNA sequences reveal that Ph. tuberculata is sister to a clade containing Dendragama, Lophocalotes, and insular Pseudocalotes. Phoxophrys tuberculata is only distantly related to Bornean congeners. Phylogenetic analysis of 29 morphological characters scored for all the species of Phoxophrys and a diverse set of 22 outgroup taxa found four well-supported lineages: Ph. tuberculata, a clade of all Bornean congeners, Ph. nigrilabris, and a clade of the four large Bornean species. To resolve paraphyly of Phoxophrys, we revalidate Pelturagonia Mocquard for all Bornean species of this genus. As redefined, Phoxophrys contains a single species: Ph. tuberculata of Sumatra. We describe a new species of Pelturagonia from the Meratus Range of southeastern Kalimantan. The new species is the sister species of Pe. spiniceps. Like that species, it differs from congeners in having large, dorsally projecting scales between the dorsolateral caudal crests and a postorbital process of the frontal bone reaching the postciliary ornament.