In Ria Formosa cockles (Cerastoderma edule) have traditionally been harvested with a harvesting-knife (HK). However, over the last six years there has been an increase in the use of a hand-dredge (HD) to exploit cockle beds. A comparative study on the impact of these harvesting methods on the benthic macrofauna was undertaken with the aim of evaluating the possible introduction of the hand-dredge in the fishery. Macrofaunal mortality was very low regardless of the gear. However, the total mortality resulting from using the HK was superior to the one observed for the HD. For the same fishing time the hand-dredge covers an area approximately five times greater that the one covered by the knife, with the former yielding 5 times the catch of the latter. Consequently, the use of hand-dredges increases the fishing effort, which may lead to the overexploitation of the cockle populations. Our results revealed that the immediate effect of both gears on macrobenthic communities was similar and minimal. Therefore, we believe that introducing the hand-dredge in the cockle fishery should only be authorised if other management measures, such as daily quotas, closed areas and limiting the number of fishing licenses, are implemented.