A growing concern about the depletion of marine resources due to fishing overexploitation and degradation of ecosystems has been demonstrated over the last decade. Monitoring the spatial and temporal distribution of fishing activities is an important tool for fisheries management which can also be used by other sectors such as fisheries science, public authorities, policy-makers and marine spatial planning. In this paper we introduce the first map of fishing activity at a Mediterranean scale of EU and non-EU fishing vessels, extracted using Automatic Identification System ship tracking data. Fishing activity maps were produced for three different years with a spatial resolution of 0.01° × 0.01°. As a main result, for the first time, changes of bottom trawl fishing activities between two consecutive years were map for the whole Mediterranean Sea. The results confirmed the suitability of this monitoring system to obtain reliable information on the extent of bottom trawl fishing activities. •Marine Spatial Planning needs monitoring the impact of human activities at sea.•AIS can be used as an alternative/integrative source to VMS to map fishing effort.•This manuscript confirms the suitability of AIS to describe the impact on seabed in terms of fishing tracks.•A three-year assessment bottom trawl fishing activity is provided for the whole Mediterranean Sea.•Change in bottom trawl fishing activity between two consecutive years were mapped.