Although tropical anguillid eels account for two-thirds of all species in the genus Anguilla, the information on the species diversity, geographic distribution, and life histories of the tropical eels is very limited. Recent studies suggested that accurate species identification in the tropical anguillid eels needs a validation by molecular genetic analysis after morphological observation. Two anguillid eels found in Sabah, Borneo Island, were firstly identified as Anguilla marmorata Quoy et Gaimard, 1824 using morphological analysis and further analysis of mitochondrial 16S ribosomal RNA (16S rRNA) sequences confirmed the morphological species identification. The presently reported study represents the first description of A. marmorata in Sabah, Borneo Island. One-year survey suggests that representatives of A. marmorata found in the region might belong to the North Pacific population in the westernmost distribution.