This chapter provides guidance on the collection and selection of species suitable for maggot therapy. All life stages are suitable for collection, except pupae that are generally hidden from view. Correct identification of the species that are collected and the correct selection of breeding stock is critical. Domestication of the newly established fly colony proceeds via adaptation to the insectary environment and the producers’ operating procedures. Monitoring of fly colony life history and morphological traits enables producers to manage the adaptation of flies to the insectary environment and to improve performance through selective breeding, genetic replenishment, and genetic engineering.