Serpentes (snakes) include over 3,600 described species, the biology of which remains poorly resolved in many regions. Snake diversity within Thailand likely reflects the diverse range of suitable habitats and climate conditions. A better understanding of their biology would allow a more comprehensive evaluation of species diversification, evolution, and conservation. Here, I tested both phenotypic and genetic polymorphisms of the Monocled cobra (Naja kaouthia) across its distribution range (north, south, centre, and north-east) in Thailand, examining regionally discrete populations that show variation in features of external morphology. To assess the possible influences of environment vs genetics on phenotypic variation, regional cobra embryos were incubated at different temperatures and examined through development while mtDNA sequencing was used to reconstruct a phylogeny of N. kaouthia. The results confirmed the effect of temperature on some aspects of cobra development and morphology. 32ºC was found to be the optimal incubation temperature for embryonic development. Unusual high temperatures increased the rate of development but also the occurrence of embryonic abnormalities while lower temperatures slowed development and extended the incubation period. Although the relationship between temperature and some developmental aspects is clear, there was no unambiguous link between temperature and regional traits. In contrast to the morphological results, high levels of genetic variation support a divergence between north+centre cobra populations and those in the south, recognise an endemic population on Pha-ngan Island in the south, and identify the north-eastern cobra population as a potential cryptic species. Thus the current variation in N. kaouthia is mainly a reflection of genetic difference, rather than environmental effect (as in phenotypic plasticity). By addressing the effect of temperature on development of N. kaouthia, the results also demonstrate the potential threat of rapid climatic change for the future of this and other reptiles.