We studied the morphological and genetic differences within Calotes jerdoni, a widespread species across northeast India. Our results suggest the presence of two distinct species in this region, one being Calotes jerdoni and the other being Calotes medogensis, which we report for the first time from India. We designate a lectotype for Calotes jerdoni and provided extended description based on freshly collected materials. Previously undetermined diagnostic characters were identified and are discussed here in detail. The aforementioned species show an interspecific pairwise genetic divergence of 13–14% in the ND2 mitochondrial gene.