The Antarctic region, a centre of biodiversity origin, influences deep-sea ecosystems by supplying species to distant regions. Understanding the influence of Antarctic Upper Circumpolar Deep Water (UCDW) on deep-sea eukaryotic diversity is therefore essential for outlining global biodiversity patterns. Our results showed the UCDW community exhibited ~1.5-fold higher taxonomic and phylogenetic diversity than the Caroline Basin control community and contained a substantial proportion of unique taxa across multiple eukaryotic lineages. Source tracking using the available Southern Ocean surface-water reference detected a 4.42% Antarctic-associated contribution to the UCDW community. Indicators and generalists of the UCDW community shared > 97% sequence identity with Southern Ocean samples. The community analyses suggested that the Yap-Mariana Junction choke point did not constitute a strong barrier to connectivity between adjacent basins, consistent with UCDW-mediated dispersal into the Philippine Basin. The UCDW microbial dispersal into the Philippine Basin occurs through two potential routes: directly through the YMJ at 2000-3000 m and via upwelling across seamounts at 500-750 m. Governed mainly by neutral, dispersal-driven processes, the UCDW community showed strong genetic exchange and connectivity. These findings suggest a role for deep-water circulation in shaping the diversity and distribution of eukaryotes detected in western Pacific deep-water samples.