Here we describe a new species of Lancehead (Bothrops jabrensis sp. nov.) based on three individuals sampled from a previously unknown population from Pico do Jabre, an isolated and small Caatinga moist-forest enclave (CMFE) located in northeastern Brazil. Although this new species has an external morphology resembling those found in representatives of the Bothrops jararaca (Wied-Neuwied, 1824) species group, B. jabrensis can be diagnosed by a combination of meristic and color characters. Molecular phylogenetic analysis indicates the new species represents a unique and highly divergent lineage within Bothrops revealing the existence of a previously unknown phylogenetic lineage that has been evolving as an independent unit for more than 8 million years. Additionally, the estimated divergence time of this lineage conflicts with some proposed scenarios of historical processes associated with the evolution of CMFEs. Finally, the uniqueness of this species indicates its relevance for the maintenance of the phylogenetic diversity of Lanceheads in South America. Like other CMFEs, Pico do Jabre is consistently threatened by poaching, illegal fires, deforestation for agricultural purposes, and illegal logging. The restricted distribution of B. jabrensis, in a small and disturbed CMFE, strongly suggests that this species is critically endangered and is likely approaching extinction as a natural population.