Muntjac deer (Cervidae:
Muntiacus) are often cited as an excellent model for the study of vertebrate evolution due to their fast rate of change in chromosome number among vertebrates. However, the phylogenetic relationships within
Muntiacus generally, and the taxonomic status of
Muntiacus gongshanensis specifically, remain unclear. Here, the phylogenetic relationships within
Muntiacus were studied using mitochondrial genome (mitogenome) and cytochrome
b (cyt
b) segments. Our results recognize 12 species within
Muntiacus and support the controversial species
M. gongshanensis,
M. putaoensis
, and
M. malabaricus. Furthermore, Bayesian inference (BI) and maximum-likelihood (ML) approaches revealed
M. gongshanensis and
M. crinifrons
to be closely related species, with
M. feae
as their sister species, and
M. putaoensis and
M. truongsonensis
to be closely related, with
M. rooseveltorum
as their sister species. The distribution range of
M. gongshanensis was also confirmed in southwest China (Namdapha, Modong, Zayu and Gongshan) and northern Myanmar (Putao). The results of this study provide insight into the evolution of
Muntiacus and further provide a molecular basis for the taxonomic evaluation of the genus in the future and fundamental data for the conservation of
M. gongshanensis.