The Old World screwworm (OWS) fly, Chrysomya bezziana, is an obligate parasite of livestock, and the myiasis caused by its larval infestations is economically important in Indonesia. The current spatial distribution of such a pest depends on two main factors: the current environmental conditions in which it can survive; and, its ability to occupy those environments by dispersal, which can be inferred from phylogeography and population genetics. These indicate that all OWS flies in Indonesia have mitochondrial cytochrome b (cyt b) haplotypes of the Asian lineage, and the regional separation of its four sub-lineages is the result of infrequent long-distance dispersal. We report the first investigation to associate regional cyt b sub-lineages of the OWS fly with environmental variables. Principal Components Analysis was used to demonstrate that these sub-lineages are associated with very similar macro-climates throughout Indonesia. Then, a species distribution model for the OWS fly in Indonesia was obtained by using the Maxent program. This indicated that elevation captured information not given by other environmental variables, and cattle density provided the most useful information by itself. The results of our study provide some important leads for future research, which will require better, stratified sampling.