Aims: To study the effect of ova disinfection, antibiotic and microbial treatments on the dominant cultivable cod rearing microbiota at pre-and posthatch stages, determining some virulence-related phenotypic traits among bacterial isolates and their relation to larval survival. Methods and Results: Sampling of rearing systems (rearing water, ova, larvae, feeds and supplement) for analysis of cultivable microbiota took place at early stages in 2004 and 2005. Cultivation, phenotypic and genotypic (16S rRNA gene) analyses were performed. The production of putative virulence factors (PVFs), including haemolysin, siderophores and quorum-sensing signals, by bacterial isolates was investigated and related to larval survival. The study was performed during two spawning seasons, evaluating current hatchery practices (ova disinfection and antibiotic treatment of unhealthy larvae) and specific putative probiotics applied to ova and larvae or rotifers. A diversified microbiota (75 operational taxonomic units, OTUs) was observed in cod rearing systems influenced by the feeds and treatments, with prevailing gamma-Proteobacteria prior to hatching towards a multiphyla microbiota posthatch. Phenotypic tests demonstrated the heterogeneity within some OTUs. Multivariate analysis of survival data in larval silos and the corresponding larval microbiota was used to divide the genotypic groups into beneficial/harmless and detrimental/opportunistic clusters. PVFs were common among the proposed detrimental/opportunistic OTUs. Conclusions: The results clearly demonstrate the influence of exogeneous feeding and treatments on larval gastrointestinal microbiota and the role of bacteria in larval survival. Significance and Impact of the Study: Increased understanding of the microbiota in rearing systems may contribute to successful implementation of microbial management in cod aquaculture.