Abstract. An extensive survey of the benthic fauna was carried out at two neighbouring regions of the Aegean Sea, one normally trawled and the other closed to trawlers. Benthic samples were collected from seven areas located away from land‐based sources. The faunistic analysis showed that species diversity and abundance was higher in the trawled area compared with the untrawled area, a fact which was attributed to the difference in sediment characteristics between the two areas. A degree of disturbance detected in the trawled area was evidenced by an increase in the number of polychaetes at the expense of other benthic groups and an abundance of some opportunistic species. This could possibly be related to trawling activities. as no other causes of disturbance were found in either area.