During the post breeding season, anuran tadpoles are subjected to a wide range of environmental variables due to intermittent dry spells leading to pond desiccation. To avoid these harsh conditions, anurans accelerate rate of metamorphosis. In anurans, hypothalamic corticotropin-releasing factor (CRF) senses stress and activates metamorphosis via hypothamalo-pituitary- interenal/thyroid axis. Cocaine and amphetamine regulated transcript peptide (CARTp) is widely reported in the brains of vertebrates except reptiles. Role of CARTp along with CRF in mitigating the physiological effects of stress in mammals is well established. Therefore, we investigated effect of puddle desiccation on the CARTp and CRF peptide immunoreactivity in the brain of prometamorphic tadpoles of Euphlyctis cyanophlyctis. Animals in the naturally occurring desiccating puddle were fixed on field and the expression of CARTp and CRF were studied using immunohistochemistry. CARTp-immunoreactivity in entopeduncular nucleus (AEN and PEN), nucleus medialis septi (NMS) and hypothalamus (dHy and vHy) significantly increased in the prometamorphic tadpoles exposed to puddle desiccation as compared to controls. In preoptic area (POA) and Edinger Westphal nucleus (EW) significant increase in CARTp as well as CRF immunoreactive cells were observed in puddle desiccation group. Strong CRF immunoreactivity was observed in median eminence of stressed group. Puddle desiccation induced increase in the expression of CARTp and CRF peptide in the neuroendocrine axis may suggest their involvement in environmental stress induced accelerated metamorphosis. Moreover, elevated expression of CARTp but not CRF peptide in regions regulating energy homeostasis may indicate starvation due to scarcity of food or stress induced appetite suppression.