Measuring and understanding patterns of beta-diversity remain major challenges in community ecology. Recently, beta-diversity has been shown to consist of 2 distinct components: (1) spatial turnover and (2) species loss leading to nestedness. Both components structure deep-sea macrofaunal assemblages but vary in importance among taxa and ocean basins and with energy availability. Here, we present the first evidence for turnover and nestedness along a bathymetric gradient in 2 major megafaunal taxa, holothurians and asteroids. Turnover is the dominant component of beta-diversity throughout bathyal and abyssal zones in both taxa, despite major differences in alpha-diversity and trophic composition. High spatial turnover suggests a role for evolutionary adaptation to environmental circumstances within depth bands. This pattern differs fundamentally from those in some macrofaunal groups in low-energy environments where abyssal nestedness is high and diversity low, with diversity maintained partly by source-sink dynamics.