Macro and meiobenthic communities of two fishing areas (Vilamoura and Lagos) in the western part of south Portugal (Algarve coast) were analysed. Both locations had been under severe dredge-fishing impact until four years previously. Vilamoura has since continued to be dredged, while fishing activity in Lagos was stopped in 1995 as a response to overfishing. For each location, three replicate areas were analysed at depths of 7–9 m. In each of these areas, 18 quadrats for macrofauna and 12 cores for meiofauna were randomly sampled by SCUBA divers during September 1999. The Shannon–Weiner diversity index was higher for meiofauna in the fished area, whereas macrofauna diversity was higher in the recently non-fished area. Bray–Curtis dissimilarity between the two areas was 87·82%. Major differences were found between Ampeliscidea, Amphiura mediterranea, Spisula solida, Haustoriidae, Nemertinea and Diogenes pugilator populations at the two sites. There was higher abundance but lower biomass of potential macrofaunal scavengers in the fished area, and carnivore biomass was also higher in this area. Deposit-feeders dominated meiofauna abundance in both study areas. The community structure of the continuously fished area was dominated by small, opportunistic, short-lived species while the community structure of the recently non-fished area was dominated by more fragile and long-living sessile organisms.