A new species of Ctenosaura is described from the Pacific versant of southeastern Honduras (Departments of Francisco Morazán and Choluteca). This species occurs in a restricted area between the ranges of Ctenosaura flavidorsalis (southwest Honduras, El Salvador and southeastern Guatemala) and Ctenosaura quinquecarinata (Nicaragua and Costa Rica). The new species differs from C. quinquecarinata, Ctenosaura oaxacana, and C. flavidorsalis in several scalation and osteological characteristics and coloration pattern. The suggested phylogenetic relationships of the new species are ((C. flavidorsalis Ctenosaura sp. “southeastern Honduras”) (C. quinquecarinata C. oaxacana)). The specimens of the new species were mostly found in hollow trees and branches no more than 2 m above the ground. The habitat was dominated by shrub and tree vegetation. This lizard feeds mainly on young leaves and insects. Local people occasionally hunt the ctenosaur for food and consider it to have become rarer in the last two decades, primarily because of habitat loss.