Subgenus Coelomys. Dao (1978) described mocchauensis as a subspecies of M. pahari. Chromosomal features of Thai samples reported by Gropp et al. (1973); 2n = FN = 48. Relationships within Mus assessed by sequences of the Sry gene (Graur, 1994); forms clade basal to species in subgenera Nannomys, Pyromys, and Mus according to study of Sry and five other genes (Lundrigan et al., 2002) and DNA/DNA hybridization experiments (Chevret et al., 2003). The close association between M. pahari and M. crociduroides and placement in subgenus Coelomys is supported by analysis of mitochondrial 12S rRNA sequences (Chevret et al., 2003). Those two species and M. mayori belong in a clade as indicated by analyses of morphological traits (Chevret et al., 2003; J. T. Marshall, Jr., 1977b). Sequences of APRT gene used to illuminate substitution rate variation among M. pahari, M. spicilegus, and other muroids (Fieldhouse et al., 1997). Ecology of population in S Yunnan and comparisons with species of Rattus, Bandicota, Maxomys, Leopoldamys, and Niviventer from the same forests reported by Wu et al. (1996).

Documented in middle and late Pleistocene cave sediments from the Sichuan-Guizhou region (Zheng, 1993) and Guangxi (Chen et al., 2002) of S China. Isolated molars from cave deposits in Thailand indicates the species was present in that region since the middle Pleistocene (Chaimanee, 1998).