Species diversity, faunal composition and abundance in the deep-sea macrobenthos are investigated at two, adjoining deep-sea areas off Portugal experiencing contrasting hydrodynamic conditions in order to test for the importance of disturbance in structuring the community. The first was located at 5,035 m depth on a presumably low current-energy site on the Tagus Abyssal Plain (TAP) and the second was centered in the lower end of the Setubal Canyon (SC) at 3,400 m depth where high levels of hydrodynamic activity are inferred from ripple bedforms visible in sea bed photographs. Closely grouped, transponder-mapped, “vegematic” box core samples were taken at each site. Agglutinated foraminifers numerically dominate the macrofauna (retained by 300 μm sieve) at both sites. Seagrass content in the SC cores indicates downslope detrital input from shallow water which is absent in the TAP samples. This must contribute, possibly with high levels of resuspended particles in near-bed flow, to the almost tenfold difference in abundance of metazoan macrofauna at the two sites. Expected species diversity measured from rarefaction is highest at TAP, both for pooled data and when foraminifers. tanaids and bivalve are considered separately. Evenness (equitability) in species' abundances is also higher at TAP than at SC. These differences are compared with benthic community data from the hydrodynamically disturbed High Energy Benthic Boundary Layer (HEBBLE) site on the Nova Scotia continental rise, and from the Rockall Trough (N.E. Atlantic). In common with these sites, strong bed flow at SC is thought to result in relatively high abundances, lower species richness and greater unevenness by acting to periodically disturb and reduce populations. Differences in the degree to which different faunal groups seem to be affected might be related to differences in lifestyle, particularly burrowing depth.