Seagrass beds, mangroves, and coral reefs are known as the three typical offshore marine ecosystems on earth. Seagrass beds, which possessing extremely high ecological service functions and are hailed as the "lungs of the ocean". Seagrasses have a relatively high level of primary productivity and play a core role in maintaining the balance and stability of the marine ecosystem. The rhizosphere eukaryotic microorganisms are crucial for seagrass growth and development, playing a crucial role in sustaining seagrass health and facilitating the cycling of nutrients such as carbon and nitrogen within the ecosystem. In this study, high - throughput sequencing technology was employed to investigate the community structure and diversity of eukaryotic microorganisms in the rhizosphere of Ruppia sinensis, Zostera marina, and Zostera japonica along the coastal areas of Shandong Province. The results showed that eukaryotic microorganisms associated with seagrasses were mainly composed of algae, metazoans, and protozoa, with Chlorophyta and Annelida being the dominant groups. The community structure of eukaryotic microorganisms in the seagrass’s rhizosphere was significantly correlated with the total carbon content, nitrite content, ammonium content, and sediment particle size. Co-occurrence network analysis further revealed that the interactions among eukaryotic microorganisms in Zostera japonica were more complex. This study elucidates the community structure and influencing factors of eukaryotic microorganisms in the seagrass rhizosphere, which laying a theoretical foundation for further exploration of the nutrients cycle and energy flow in seagrass ecosystem.