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Worldwide, there are over 1000 species of blow flies (Diptera: Calliphoridae). Blow flies display a variety of habits, however they are best known for their role in the decomposition of carrion. As yet, there are few studies of their population genetic structure, although such data would contribute to such fields as pest management, taxonomy, forensic entomology and veterinary medicine. Although it is typically assumed that carrion fly populations are panmictic, this has been disputed. This research focused on developing a new protocol to understand the population genetic structure in carrion flies using amplified fragment length polymorphism (AFLP) profiles. My specific objectives were to develop and validate an AFLP protocol for use in a sampling of calliphorid flies visiting carrion and to use AFLP loci to establish the degree of spatial and temporal genetic variation in two common species of Calliphorid flies (Lucilia sericata Meigen and Phormia regina Meigen). On a wide geographic and temporal scale, the population structure of these two carrion flies are panmictic, but individual samples represent a non-random sample of the population (individuals within a sample were highly related to one another, R>0 in all cases). This research also demonstrated a correlation between the number of individuals collected in a sample to the overall relatedness of the samples genotyped. In addition, the use of a lab generated pedigree of P. regina was used to design an empirical test for full sibship, which can then be useful in the interpretation of postmortem movement of a corpse. A final objective of this work was to develop a protocol for assignment methods with AFLP loci chosen to resolve closely related carrion fly species previously unresolved using other genotyping systems. This was successfully demonstrated using two species of African chrysomyinae blow flies (Chrysomya putoria and Ch. chloropyga) and a group of Protocalliphora spp. blow flies.