Parastic dinoflagellates Syndiniales, a group of parasitic marine alveolates, are gaining recognition for their ecological role, but their diversity and spatiotemporal dynamics in tropical coastal waters are largely unexplored. Here, we present the first comprehensive study of Syndiniales diversity, utilizing high-throughput sequencing (HTS) of the small subunit ribosomal DNA (SSU rDNA) V4 region, coupled with size-fractionated sampling (0.2–3 µm and ≥3 µm) in Sanya Bay over the period 2019–2021. The results reveal remarkable genetic diversity across Syndiniales group I-V, including the discovery of seven novel clade alongside the previously described 35 clades in Group II and 5 clades in Group I. We demonstrate strong correlations between Syndiniales abundance and environmental factors, particularly temperature and nutrient availability, through spatial and temporal analyses. Additionally, network analysis indicates potential host-parasite interactions between Syndiniales and dominant dinoflagellate taxa, offering new insights into their ecological roles. This study not only confirms the SSU rDNA V4 region as a valuable molecular marker for investigating Syndiniales diversity but also provides the first comprehensive characterization of its genetic diversity and temporal dynamics across seasonal cycles in marine ecosystems.