The Araripe Manakin (Passeriformes: Pipridae: Antilophia bokermanni) is the most threatened passeriform species and is classified as critically endangered. With an estimated population of only 800 individuals, this species is endemic to a small area (∼30 km2) of forest on the slopes of the Araripe Plateau in northeastern Brazil. The urgent need to implement an effective conservation program for the Araripe Manakin has stimulated intensive research into various aspects of its biology. We sequenced a segment of the mtDNA between the genes ND6 and 12S rDNA, which includes a pseudo-control region. This region was analyzed in 30 specimens of A. bokermanni with the aim of measuring intraspecific genetic diversity and population structure. Although the segment's position is the same as described in other bird species, A. bokermanni differs in some aspects, such as its length of 200 base pairs and the absence of indels or tandem repeats. Our analysis provides no evidence of population substructuring or a history of population expansion. The species' genetic variability is slightly reduced in comparison with its sister species A. galeata, but their similarity indicates a relatively recent process of separation.