We describe a new species of small-sized Calotes from mid-elevation (~1270 m asl.), swidden or shifting cultivation areas in the Subansiri river basin, Upper Subansiri District, Arunachal Pradesh, India. Mitochondrial sequence data (ND2) recovers Calotes sinyik sp. nov. as the closely related sister taxon to an unnamed species from Medog, Tibet; the two falling in a broader clade including C. paulus + C. zolaiking and species of the C. emma and C. mystaceus groups. The new species is 7.8% divergent in ND2 sequence data from the unnamed lineage from Medog and deeply divergent (≥ 21.6–28.1%) from other congeners. The new species can easily be distinguished from regional congeners by its small adult body size (maximum snout to vent length of 65 mm) and heterogenous dorsal scales, and from its closest relatives C. paulus and C. zolaiking by having 54 or 55 midbody scale rows and 42 or 43 vertebral scales. It is likely that many more allied species remain to be discovered from Northeast India, which remains poorly surveyed across taxonomic groups.