The Christmas Island flying fox (Pteropus melanotus natalis) is thought to be declining to critically low levels. Mitochondrial sequences of the cytochrome oxidase 1 (CO1) and cytochrome b (Cytb) genes and the D-loop were generated from 28 animals and used with maximum likelihood, Bayesian inference, and maximum parsimony methods to determine its relationship to other Pteropus species. In all analyses, P. m. natalis mapped to a large clade containing Pacific Ocean island and Australian Pteropus species. Analysis using the large numbers of available Cytb sequences for Pteropus showed that P. m. natalis maps to a subclade that contains P. hypomelanus sequences from bats originating from Pulau Panjang, an island off the northeast coast of Java. P. hypomelanus was found to be polyphyletic, mapping to 3 separate subclades. These 3 genetically and geographically defined populations are likely to represent 3 separate species. Eighteen D-loop haplotypes were identified, suggesting that P. m. natalis maintains a degree of genetic diversity similar to other insular flying fox species.