The green blowfly, Lucilia sericata (Meigen) (Diptera: Calliphoridae), is a cosmopolitan species of great medical, veterinary, and forensic importance. In addition, their larvae are among the most promising agents for the bioconversion of low‐quality biomass, such as organic waste, into sustainable and nutritionally valuable proteins for farmed fish and poultry. Despite the considerable medical and economic importance, the current literature provides limited information about microbiota associated with larvae. The present study aims to fill this knowledge gap. Freshly harvested L. sericata larvae (maggots) grown on fish wastes were investigated by conventional and molecular approaches to evaluate culturable microbial numbers and unculturable microbial diversity associated with the larval cuticle (external samples) and the internal body. In total 200 bacterial isolates were obtained; 46% of the strains originated from external samples and 58% originated from internal body samples produced extracellular protease enzymes, which may be involved in the digestion of proteins during larval feeding. In total 12 predominant bacteria with high proteolytic activity were further identified by morphological, physiological, biochemical, and molecular tools. Proteolytic bacteria in internal samples included Proteus, Providencia, Micrococcus, Deinococcus, whereas in external samples Providencia, Pseudomonas, and Acinetobacter were found. 16S rRNA clone library analysis revealed that the majority of internal bacteria (35%) were taxonomically assigned as Xanthomonadaceae (Schineria, Xylella, Ignnatzchineria), 28% Morganellaceae (Proteus, Providencia, Serratia), and 14% Enterobacteriaceae (Vagococcus, Serratia). Less abundant were bacteria of the genera Clostridium (3%), Erypelothrix (3%), and Oceanispherum (2%). This knowledge will be useful for biotechnological application of L. sericata.