The Balimo region of Western province Papua New Guinea (PNG) is a recently described remote hot-spot for melioidosis. Molecular epidemiology has revealed that Burkholderia pseudomallei isolates from this region demonstrate narrow genetic diversity, yet have the characteristics of long term separation. A study was conducted to compare isolates from this region and the neighbouring endemic regions in PNG and Nth Queensland, including the Torres Strait Islands (TSI), to determine if any relatedness between these isolates could be demonstrated and if so if these associations could inform the origins and movement of B. pseudomallei within this region. Sequence information from 78 isolates from Balimo, TSI, Port Moresby (POM) and mainland Nth Queensland generated from MLST analysis and genotyping of the fimbrial gene cluster were compared. Phylogenetic analysis by eburst demonstrated that all isolates belong to the Australian clade, although many expressed the YLF (Asian) rather than the BTFC (Australian) fimbrial genotype characteristic. Further analysis of the whole genome sequence of a selected number of the isolates demonstrated that those from Balimo were more likely to be related to those of the TSI rather that POM which is consistent with dispersal influenced by ancestral human migration. Also, an increased diversity of STs was demonstrated from regions where human movement is more intense and STs from the TSI which are less frequented seem to cluster. These results support a non-random dispersal hypothesis of B. pseudomallei associated with ancestral and recent human movement and provide evidence of likely island biogeography.