BACKGROUND: Spatio-temporal patterns on benthic molluscan macrofauna structure and function (feeding guilds) were investigated in a commercial fishing ground in Thermaikos Gulf (N Aegean Sea). Fishery management measures in this area include a trawling period of 8 months per year (October to May). Macrofauna samples were collected before and after 30 and 120 days of the commencement of the trawling period (temporal axis) along a southward transect (spatial axis) and down through the sediment profile (vertical axis).RESULTS: Main results revealed no recognizable changes in community diversity and structure at temporal scales. This finding can probably be attributed to the fact that the examined communities are subjected to continuous disturbances deriving from multiple natural and anthropogenic stressors acting simultaneously in Thermaikos Gulf. Molluscan assemblages were already stressed before the commencement of the trawling period, indicating that the time period in which bottom trawling is prohibited is not sufficient for the recovery of benthic communities. Significant shifts in the trophic structure of molluscan assemblages were also detected. The direct mortality of herbivorous species and the loss of filter feeding organisms may be attributed to the passage of the fishing gear and to sediment re-suspension, respectively. Trawling disturbance may have created the observed vertical patterns of the community structure since hauling induces profound changes in the geochemical profile of the sediment.CONCLUSIONS: Our findings sustained the notion that bottom trawling, alongside with other types of human induced stressors, can have considerable effects on the structure and function of the benthic domain. Therefore, our results highlighted the need of an Ecosystem Based Fishery Management (EBFM) perspective in Thermaikos Gulf to ensure both fisheries and ecosystem sustainability.