The Juan Fernandez Firecrown Sephanoides fernandensis is an endangered endemic hummingbird that inhabits the Juan Fernandez Islands, 667 km off the coast of Chile. Its population has decreased from several thousand in the early part of this century to approximately 250-400 individuals at present. The reasons for its decline include habitat degradation by anthropogenic forest clearance and the introduction of grazing mammals and rodents. Another hummingbird, the Green?backed Firecrown Sephanoides sephaniodes, inhabits the Juan Fernandez Islands but is also found on the Chilean mainland. It currently numbers several thousand on the Juan Fernandez Islands but was considered rare during the late 19th and early 20th centuries. The sister relationship between the two species has not been critically tested, and so their evolutionary histories on the Juan Fernandez Islands remain uncertain. With the use of mtDNA cytochrome b and ND2 phylogenetic reconstructions, our study supports the two species as sister taxa. Moreover, the molecular data suggest that the genus Sephanoides is closely related to the higher altitude Andean hummingbirds typical of the paramo and puna habitats. The molecular divergence between the two species of Sephanoides indicates they may have become isolated from each other less than 1 million years ago, suggesting that S. fernandensis evolved in situ on the Juan Fernandez Islands. We find no evidence of genetic subdivision between populations of S. sephaniodes from the Juan Fernandez Islands and the mainland. In addition, high genetic variation of the Juan Fernandez Islands population does not indicate a long period of isolation of a limited number of S. sephaniodes but instead suggests a recent colonization event, perhaps from several mainland populations. As a result of molecular, morphological and apparent ecological similarities, we suggest that competition by S. sephaniodes may be an additional factor stifling the recovery of S. fernandensis. Possible conservation strategies include habitat restoration and the removal of introduced mammals; immediate implementation of such conservation management plans are necessary to save this species from extinction.