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The black soldier fly (Hermetia illucens) has gained increased importance as a prime candidate for industrial production of alternative animal protein production and biowaste recycling. Optimisation of rearing management of this emerging industry requires a better understanding of how biotic factors, mainly host-microbiota interactions, affect the insect health and growth performance. This investigative study seeks to characterise microbiota associated with H. illucens across the entire life cycle (eggs, larvae, prepupae and adults) when reared in two substrates: i) plant-based (Housefly Gainesville diet) and ii) animal-based (poultry hatchery waste). We used a metataxonomic approach with 16S and 18S genetic markers amplicon sequencing, the latter made possible by the development of a blocking primer specific to the black soldier fly. This enables for the first time to produce a comprehensive profile of H. illucens microbiota encompassing a wide diversity of eukaryotic microorganisms, often neglected in microbial studies. The microbiota was sampled for two generations, from parents (X0) to all progeny’s developmental stages until maturity (X1). ASV tables issued from amplicon sequencing are now being investigated to compare taxonomic and functional profiles, diversity and dynamics of populations and to reveal interactions networks within said profiles. We hypothesize the existence of a core microbiota that will be partly inherited from parents and remains stable throughout development, and we also expect the overall microbiota to be modulated by the feed substrate, developmental stage, and time. We further hypothesize that individuals not reared on the same substrate as their parent will display a greater divergence in core microbial composition and potential signs of dysbiosis in early stages. These preliminary results are expected to be completed in September. Our study will give insight into how H. illucens health and performance could be managed using probiotic supplements.