Management solutions for waste in southern Thailand, such as fly larvae, are tested in a laboratory using different substrates and wastes from the Thai agricultural sector. The nutritional content of the immature stages of Musca domestica Linnaeus (Diptera: Muscidae) and Hermetia illucens (Linnaeus) (Diptera: Stratiomyidae) larvae, especially their protein and fat contents, makes them a potential animal feed. Laboratory strains of M. domestica and H. illucens were reared on selected substrates to examine how diet influenced their performance and nutritional composition. Waste from aquaculture, vegetables, and fruits in southern Thailand was examined for larval diet and showed promise as a rearing substrate for these insects. Musca domestica larvae reared on fishery waste achieved the highest larval weight and fat content, whereas H. illucens larvae reared on an aquaculture waste diet had the highest protein content.These findings imply aquaculture waste could be the best choice for large-scale fly larvae production, particularly as a protein feed additive.