The presence of a challenging microbial flora in larval rearing systems of the ornate rock lobster, Panulirus ornatus, requires the evaluation of suitable options for microbial management. Larval rearing on a commercially viable scale can only be established with a controlled microbial environment, since the proliferation of pathogenic and/or biofouling bacteria contribute to high mortalities of captive-reared larvae. In the present study, the bacterial colonization of three microbial compartments of an aquaculture larval rearing system of Panulirus ornatus was investigated and microbial management options for each compartment analyzed. Biofilm: Ozonation significantly modified the temporal progression of biofilm development and favoured the dominance of γ-Proteobacteria within the biofilm community, of which some dominant sequences showed most similarity to coral-associated bacterial strains. Ozonation delayed the establishment of filamentous bacteria, and also repressed the proliferation of pathogens and sulfur-metabolizing bacteria. The various effects of ozonation illustrated the presence of complex interactions during the process of bacterial colonization. Thus, the experiment highlighted the dynamics within the microbial community. Artemia: The distinct Vibrio load of Artemia demonstrated their potential as a vector of pathogenic bacteria to phyllosoma rearing. This potential was shown to be increased with older animals. Only a mixture of three different antibiotics reduced their load with cultivable vibrios. Concurrently, the problem of antibiotics resistance was underlined. The analysis accented the inadequacy of antibiotics for effective microbial management. At present however, alternative treatments cannot rely on commercial probiotics, whose poor efficiency was demonstrated likewise. Phyllosoma: The bacterial colonization vastly differed between cultured and wild phyllosoma. This confirmed the enhancement of biofouling processes in closed rearing environments, which was illustrated by the increased external attachment of filamentous and rod-shaped bacteria at the mouthparts and anus. The bacterial colonization of wild, healthy larvae was low, and comprised a diverse community including the Vibrionaceae. Thus, a presence of Vibrio-affiliated strains was separated from the occurrence of disease. Three bacterial isolates from wild larvae were demonstrated as inhibitory towards a pathogenic Vibrio strain and could represent probiotic candidates for implementation in phyllosoma rearing.