Ecosystems face various pressures, often leading to loss of biodiversity. Understanding how biodiversity is spatially structured, what are the driving factors, and the ecological and evolutionary processes involved is essential to assess communities' resilience to disturbances and guide efficient conservation measures. Hydrothermal vents from national waters of the West Pacific are targeted by mining industries for their mineral resources that include metals used in high-tech equipment. Although exploitation has not yet started, such activity could significantly affect ecosystem biodiversity and functioning. Here, we describe the distribution of hydrothermal biodiversity in the Southwest Pacific back-arc basins and the Futuna Volcanic Arc at different spatial scales in relation to environmental conditions and geography. We focused on three assemblages dominated by symbiotic megafauna: snails (Alviniconcha spp. and Ifremeria nautilei) and mussels (Bathymodiolus spp.). Faunal assemblages exhibit strong spatial structuring: between habitats along the dilution gradient of the hydrothermal fluid, and between geographic basins, with a faunal split between the Western and the Eastern basins of this region, and to a lesser extent, between fields in a basin. Species replacement along the chemical gradient drives faunal changes between Ifremeria and Bathymodiolus assemblages, while a drop in the number of species is noted when making this comparison with the Alviniconcha assemblage. While these local changes may result from environmental filtering along the diffuse flow gradient, geological settings and current geographic barriers, which drive colonization and speciation at larger scales, are likely shaping the vent community changes between the Eastern and Western basins. This result has significant implications for biodiversity conservation, especially in this mineral-rich setting. The Manus Basin is isolated and displays the highest proportion of endemism while the Woodlark Basin represents an important stepping-stone between the Eastern basins and Manus Basin, making them potentially highly vulnerable to mining with a risk of biodiversity loss.