A portion of mitochondrially encoded 12S and 16S ribosomal RNA genes were sequenced from all four valid species of the midwater deep-sea fish genus Sternoptyx (Teleostei: Sternoptychidae) and four sternoptychid outgroup taxa. Secondary structure-based alignment resulted in a character matrix consisting of 865 bp of unambiguously aligned, combined sequences of the two genes, which were subjected to phylogenetic analyses using the maximum parsimony and maximum likelihood methods. The resultant tree topologies from the two methods were congruent and supported by various tree statistics. Although the single most parsimonious tree was not statistically different from the two second parsimonious trees, independent morphological evidence from the anal fin pterygiophore configuration and associated structures strongly supported the former as the preferred hypothesis. Mapping of the contemporary geographic distribution patterns of the four species onto the tree suggested that there was a common ancestor of Sternoptyx with a circumglobal distribution, which had been subdivided into southern and northern ancestral populations along 30 degrees S, possibly through some large-scale oceanographic event. There has been no discernible speciation event in the southern population, though the northern population has subsequently speciated into three contemporary species with largely allopatric/microallopatric distributions.