Burkholderia pseudomallei is an infectious Gram-negative bacterium that causes melioidosis, a disease of high mortality if untreated. Multilocus sequence typing (MLST) is a popular and portable genotyping method, used extensively to characterise the genetic diversity of B. pseudomallei populations. MLST has been central in our understanding of the underlying phylogeographic signal present in the B. pseudomallei genome, with distinct populations observed on both the intra- and inter-continental level. However, due to the high recombination rate of B. pseudomallei, and the inherit limitations of MLST, it is possible for isolates to share the same multilocus sequence type (ST) even though they are genetically and geographically distinct, with two cases of ST homoplasy reported in Asian and Australian B. pseudomallei isolates to date. Such spurious results can dramatically confound conclusions about disease transmission and attribution. Therefore, it is import identify instances of ST homoplasy using higher-resolution genotyping methods. In this study, we used whole-genome sequencing to identify two cases of intracontinental ST homoplasy from environmental B. pseudomallei isolates separated by large (>400km) geographic distances. We also identify a long-range (460 km) dispersal event of a single ST between a remote Australian island and the Australian mainland. Our results show that, whilst a highly useful and portable method, MLST can lead to erroneous conclusions about isolate origin and disease attribution. In cases where a shared ST is identified between geographically distant locales, whole-genome sequencing should be used to resolve strain origin.