<p>Extremely high mortality during early juvenile development remains the primary constraint to establishing sustainable aquaculture protocols for threatened seahorse species (<i>Hippocampus</i> spp.). Despite sustained efforts focused on nutritional optimisation, water quality control and pathogen suppression, survival rates have improved only marginally, suggesting that key underlying drivers remain insufficiently addressed. This conceptual review posits that juvenile mortality fundamentally constitutes a microbial ecological challenge, in which conventional rearing environments generate dysbiotic states that selectively favour opportunistic pathogens while failing to support protective microbial communities. Here we propose a microbiome-centric conceptual framework that reconceptualises the larval rearing unit as a dynamic microbial ecosystem, in which biofilm formation, microbial succession and host-microbe interactions collectively shape disease risk and larval survival. By integrating insight from biofilm ecology, probiotic research and biofloc technology, we synthesise dispersed findings to interpret larval mortality as an emergent outcome of disbiotic rearing environments, rather than isolated pathogenetic events. Emphasis is placed on ecological mechanisms, such as niche preemption, competitive exclusion and quorum quenching, rather than on taxonomic inventories of candidate probiotics. Finally, we translate this framework into a structured research agenda by identifying key knowledge gapes, testable hypothesis and operational implications for hatchery practices. By shifting the focus from pathogen eradication to microbial ecosystem engineering, this conceptual synthesis provides a foundation for more resilient and predictable seahorse aquaculture systems, offering a perspective applicable to other sensitive marine larval cultures.</p>