Recent advancements in deep-sea expeditions have made possible to sample adequate quantities of deep-sea organisms over wide geographical ranges for population genetic studies. Scalpellum stearnsii is a common stalked barnacle that occurs in the mesobenthic environment (>200 m depth) throughout the West Pacific Ocean and covers several major deep-sea basins. The present study examined the diversity and genetic differentiation of S. stearnsii populations from the East China Sea, West Philippine Basin, Sulu Sea, and Caroline Trenches. Molecular analyses based on partial sequences of the mitochondrial gene COI and nuclear gene H3 revealed four distinct clades of S. stearnsii—SS, CF1, CF2, and CF3—with distinct species-level pairwise divergences among the clades. SS (representing S. stearnsii, based on morphological comparison with holotype) is mainly present in the East China Sea and the Philippine Basin, CF1 is present in the East China Sea, CF2 is present in the Sulu Sea, and CF3 is exclusively present in the Caroline Trench (Southwest Pacific Ocean). Deep genetic differentiation between the northern (SS and CF1) and southern clades (CF2 and CF3) was estimated to have occurred around 33 million years ago, and the eastward-flowing Equatorial Undercurrent (100–200 m) and oxygen minimum zone (300–400 m) are the putative barriers to gene flow. The timing is concordant with reported diversification events in both shallow- and deep-water organisms during the Oligocene and Miocene periods. This cross-ocean, -taxon, and -habitat divergence time suggests speciation driven by global-scale events. Recent size expansion likely occurred in all the four clades and subsequent populations, predating the Last Glacial Maximum (LGM). The persistence of mesobenthic deep-sea barnacles through the temperature fluctuation at the LGM can be a common pattern.