<p>The intestinal microbiome of fish at early stages of ontogeny represents a complex and dynamic ecosystem that is critically important for immune system development, physiological resilience, and growth. The yolk-sac stage is of particular significance, as larvae rely exclusively on endogenous nutrient reserves while being colonized by microbes for the first time. During this period, the foundations of microbiota are established, which subsequently influence the development of the digestive system, barrier functions, and pathogen resistance. Recent studies show that microbial communities at this stage are characterized by low alpha diversity and the dominance of <i>Proteobacteria</i>, <i>Firmicutes</i>, and <i>Bacteroidetes</i>. With the transition to exogenous feeding, there is an increase in taxonomic and functional diversity, along with the emergence of probiotic genera (<i>Bacillus</i>,<i> Lactobacillus</i>,<i> Shewanella</i>) that promote enzymatic activity, immune modulation, and increased survival of larvae. This review systematically compiles data from the past 20 years, encompassing both culture-dependent methods and high-throughput sequencing approaches. It has been demonstrated that despite the limitations of culture-based methods, they remain indispensable for isolating probiotic strains. A comparison of methodologies revealed high variability in protocols, complicating the direct comparison of results. The findings underscore the applied significance of studying microbiota for aquaculture during the yolk-sac stage. The management of microbial communities through probiotics, prebiotics, and environmental regulation presents prospects for enhancing the survival, growth, and resilience of fish larvae.</p>