Fish eggs play a crucial role as an initial source for replenishing fish populations, with their quantity and species composition being pivotal for determining the overall fish community structure. Variations in their abundance directly impact fishery resources. Identifying and analyzing the composition of fish eggs are indispensable for understanding fish ecology and conservation efforts, offering insights into spawning locations, timing, and reproductive dynamics across multiple species. Moreover, such analyses provide a foundational understanding for studying fish resource replenishment mechanisms, population dynamics, and sustainable fisheries management. Conventionally, research on fish eggs relies on morphological techniques, which often encounter challenges in accurately identifying egg species. To elucidate the spatial distribution, species composition, and their correlation with environmental factors of early fish resources in the Daya Bay, samples were collected from 14 sites in April 2022. Mitochondrial DNA cytochrome oxidase subunit I (CO I) fragments served as molecular markers for species identification. The findings unveiled 36 species of spring fish eggs in the Daya Bay, spanning 7 orders, 16 families, and 26 genera. Notably, 31 species, 3 genera, and 2 families were identified. The mean fish egg density stood at 10.12 ind/m³ , with the highest density recorded at site S7, reaching 37.3 ind/m³ . Dominant species (with dominance≥0.02) included Nuchequula nuchalis, Gerres decacanthus, Alepes kleinii, Stolephorus insularis, Thryssa mystax, Escualosa thoracata, and Photopectoralis bindus. Environmental factor analysis revealed no significant correlation between environmental variables and the distribution of eggs from dominant species, primarily due to their eurythermal euryhaline nature, exhibiting robust adaptability to marine environments. This study highlights a predominance of small, low-value species, such as Nuchequula nuchalis, Photopectoralis bindus, and Gerres decacanthus, with an absence of eggs from high-value economic fish. Such observations mirror the prevailing trend in Daya Bay’s fishery resources, characterized by a shift towards smaller fish groups with reduced individual size and economic worth. This trend reflects the adaptive responses of fish to marine environments. Daya Bay emerges as a crucial spawning ground for diverse fish species, underscoring the imperative to enhance the protection of its fishery resources and restore the functionality of its valuable germplasm resources.