The phylogeny and species boundaries of Gazella subgutturosa and G. marica have been long debated. The achievements of past conservation efforts have been compromised by a lack of knowledge about the phylogeny and taxonomic status of different populations. We integrated the recent genetic findings by previous studies with morphometric analyses and ecological niche modelling (ENM) to assess discreteness among populations of these gazelle species in Asia. Taxonomic diversity of gazelles was investigated by using principal components analysis (PCA) based on 14 cranial measures of male skulls. Ecological niche divergence was examined based on a PCA on climatic factors and a species distribution modelling (SDM) with environmental variables. Morphometric results indicated substantial differentiation in size between skulls of the western Zagros Mountains including west and south-western Iran and Arabian Peninsula from all other samples east of the Zagros Mountains from Iran to China. ENM also revealed that gazelles in the east and west of Zagros Mountains occupy distinct niches and that there are apparent areas of disconnection across the goitered gazelle suitable range. A complete divergent niche occupation was also observed between gazelles of Mongolia and other Asiatic gazelles, except for China. Taking the inferences from ENM and morphology together with previous genetics results, we conclude that gazelles in the west and southwest of Iran may represent G. marica. Also, our combined analyses revealed divergence among gazelles of Iran, Central Asia, and Mongolia/China. These results may pave the way for future studies and have conservation implications particularly for reintroduction/supplementation programs.