The deep sea is a vast and essentially continuous environment with few obvious barriers to gene flow. How populations diverge and new species form in this remote ecosystem is poorly understood. Phylogeographic analyses have begun to provide some insight into evolutionary processes at bathyal depths (< 3000 m), but much less is known about evolution in the more extensive abyssal regions (>3000 m). Here we quantify geographic and bathymetric patterns of genetic variation (16S rRNA mitochondrial gene) in the protobranch bivalve Ledella ultima, which is one of the most abundant abyssal protobranchs in the Atlantic with a broad bathymetric and geographic distribution. We found virtually no genetic divergence within basins and only modest divergence among eight Atlantic basins. Levels of population divergence among basins were related to geographic distance and were greater in the South Atlantic than in the North Atlantic. Ocean-wide patterns of genetic variation indicate basin wide divergence that exceeds what others have found for abyssal organisms, but considerably less than bathyal protobranchs across similar geographic scales. Populations on either side of the Mid-Atlantic Ridge in the North Atlantic differed suggesting the Ridge might impede gene flow at abyssal depths. Our results indicate that abyssal populations might be quite large (cosmopolitan), exhibit only modest genetic structure and probably provide little potential for the formation of new species.