We describe a new species of Cnemidophorus from a Cerrado enclave in southwestern Amazonia, Rondônia state, Brazil. This species is apparently endemic to Cerrado enclaves in the vicinity of the city of Vilhena, a region under intensive anthropic pressure due to the expansion of soybean plantations. A discriminant analysis indicated that femoral pores and scales around the tail are the best discriminators among Brazilian species of Cnemidophorus. A naïve Bayesian network constructed with categorical (mostly coloration) variables indicated that the new species had high conditional probabilities of dorsolateral fields absent, vertebral field spotted, and paravertebral lines absent. The analyses revealed clear distinctions between species of Cnemidophorus that range north and south of the the Amazon River. The new species may have evolved as a result of vicariance, following the isolation of peripheral enclaves of Cerrado in southwestern Amazonia after the late Pleniglacial. The restricted range in small areas, under extreme human pressure around Vilhena, makes this species one of the most critically endangered elements of the Brazilian herpetofauna.