<p>Population genetic patterns and changes in allele frequency within blow flies can provide valuable insight into population structure, diversification, dispersal, gene flow, and population assignments. The population genetic structure of the oriental latrine blow fly, <i>Chrysomya megacephala</i> (Fabricius), was investigated using amplified fragment length polymorphisms (AFLP). The goal was to validate the use of this technique to create genetic profile data and determine it is feasibility for inferring postmortem relocation of corpses. The AFLP technique generated 590 polymorphic loci for <i>C. megacephala</i>. Analysis of molecular variation (AMOVA) found significantly high genetic variation within individuals of all fly populations, with little variation among populations from different geographic locations. STRUCTURE and principal coordinate analyses (PCoA) revealed no population structure based on geography, with weak correlation between genetic and geographic distances, and moderate temporal differentiation was noted among <i>C. megacephala</i> samples. Across the entire data set, the mean relative relatedness coefficients were positive, suggesting that flies arriving at the same bait (carcass) share nonrandom proportions of alleles and comprise of closely related individuals. Genetic assignment of <i>C. megacephala</i> flies to a putative source population resulted in a 90.81% success rate, indicating the possibility of using these flies to connect sites between which a corpse had been moved even in the absence of overall geographic population structure.</p>