Within-island speciation may play a significant role in shaping biodiversity in a large oceanic island. Sulawesi is the largest oceanic island in the Indo-Australian Archipelago with most species evolved after crossing Wallace’s Line. Bunomys is the best representative of a unique murine radiation and distribution on Sulawesi with one species being widespread and the other species restricted to particular part of the island. Here, we used phylogenetic analyses from five independent loci to determine the systematic relationships of species in the genus Bunomys and to test the monophyly of the genus with respect other endemic murine genera from Sulawesi. We used morphometric analyses and qualitative morphological characters to determine if B. fratrorum populations across the northern peninsula of Sulawesi represent distinct species. We found that Bunomys fratrorum thought to be endemic to the eastern half of the northern peninsula are distributed to the western end of the peninsula. Our phylogenetic analyses show that B. fratrorum was not related to the other genera of Bunomys and may support to resurrecting of the genus Frateromys. Using both phylogenetic and morphometric analysis, we determine B. fratrorum may represent two divergent populations across the northern peninsula. Phylogenetic differences across the northern peninsula support the evidence for the significance of within-island speciation in producing species diversity on Sulawesi.