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The animal was again recorded at Ankaratra in 1996, this time in a heavily disturbed forest, where it occurred with Eliurus minor and the introduced black rat(Rattus rattus). At Andringitra, the animal was recorded in high montane forest together with six other nesomyines—Brachyuromys ramirohitra, Eliurus minor, Eliurus tanala, Eliurus webbi, Gymnuromys roberti, and Nesomys rufus—as well as the black rat. At Andohahela, Monticolomys was found at an altitude of 1,875 m (6,152 ft) in sclerophyllousforest. Its distribution corresponds to the High Mountain Domain, a region defined on the basis of plant distributions. This region is now discontinuous, but the High Mountain Domain habitat was continuous from mountain to mountain as recently as the early Holocene. Subfossil remains have been found in Mahajanga Province (northwestern Madagascar). Malagasy mountain mouse is morphologically uniform across its wide distribution.
It is nocturnal and solitary and produces litters of up to three offspring. It is scansorial, spending time on the ground but also climbing in vegetation. In Andringitra, two specimens were captured on a liana 2 m (6.6 ft) over the ground, and a third was caught on the ground together with two shrew tenrecs (Microgale taiva). All five specimens from Andohahela were trapped on the ground, as was the specimen caught in Ankaratra in 1996. Its diet includes fruits and seeds; in captivity, it eats Agauriafruits.