Our knowledge of the distribution and evolution of deep-sea life is limited, impeding our ability to identify priority areas for conservation. Here we analyse, for the first time, large integrated phylogenomic and distributional datasets of seafloor fauna from sea surface to abyss and equator to pole of the Southern Hemisphere for an entire class of invertebrates (Ophiuroidea). We find that latitudinal diversity gradients are assembled through contrasting evolutionary processes for shallow (0-200 m) and deep (> 200 m) seas. The shallow-water tropical-temperate realm broadly reflects a tropical diversification-driven process but with exchange in both directions. Diversification rates are reversed for the realm containing the deep sea and Antarctica, being highest at polar and lowest at tropical latitudes, and net exchange is from high to low latitudes. The tropical upper bathyal (200-700 m deep), with its rich ancient phylodiversity, is characterised by relatively low diversification and moderate immigration rates. Conversely, the young specialised Antarctic fauna is inferred to be rebounding from regional extinction associated with the rapid cooling of polar waters over the mid-Cenozoic.