Tropical mountains are cradles of biodiversity and endemism. Sundaland, tropical Southeast Asia, hosts three species of Rattus endemic to elevations above 2,000 m with an apparent convergence in external morphology: Rattus korinchi and R. hoogerwerfi from Sumatra, and R. baluensis from Borneo. A fourth one, R. tiomanicus, is restricted to lowland elevations across the whole region. The origins of these endemics are little known due to the absence of a robust phylogenetic framework. We use complete mitochondrial genomes from the three high altitude Rattus, and several related species to determine their relationships, date divergences, reconstruct their history of colonization and test for selection on the mitochondrial DNA. We show that mountain colonization happened independently in Borneo (< 390 Kya) and Sumatra (~1.38 Mya), likely from lowland lineages. The origin of the Bornean endemic R. baluensis is very recent and its genetic diversity is nested within the diversity of R. tiomanicus. We found weak evidence of positive selection in the high-elevation lineages, and attributed the greater non-synonymous mutations on these branches (specially R. baluensis) to lesser purifying selection having acted on the terminal branches in the phylogeny.