We investigated the phylogeography of the dugong (Dugong dugon) across its original range using museum material from 14 natural history museum and university collections. The mitochondrial DNA control region was successfully amplified from samples of bone or tooth powder from 162 individuals. These samples range from 1827 to 1996 and span the historical distribution range of the dugong. We were able to successfully amplify overlapping fragments of the D-loop region of the mitochondrial DNA (mtDNA) resulting in sequences of a 355 bp fragment for 162 individuals for the final analyses. This included a new sequence (189 bp) from a previously unidentified piece of skin of the extinct Steller's sea cow (Hydrodamalis gigas), as an outgroup. The resulting dugong sequences match those from previous studies of dugongs from Australia and Indonesia, but revealed several new and divergent mtDNA lineages in the Indian Ocean. One mtDNA lineage includes most specimens from the Western Indian Ocean, with another distinct lineage isolated to nearby Madagascar and Comores. There is little geographic structuring detectable among other populations in the Western Indian Ocean and all populations from that region appear to have historically contained comparatively low levels of genetic diversity. The genetic diversity of several Indian Ocean samples collected after 1950 was lower than that of the samples collected earlier from similar locations, a result coincident with the anecdotal reductions in population size. The new lineages and potential loss of diversity highlight the particular conservation importance and vulnerability of dugong populations in the Western Indian Ocean.