The dataset provided here consists of sighting data of marine mammals collected between January 2014 and December 2018, along the ferry route between Italy and Spain, within the Fixed Line Transect Mediterranean monitoring Network (FLT Med Net), a multidisciplinary monitoring project coordinated by ISPRA since 2007. The programme uses ferry boats as observation platforms to undertake surveys of marine macro-fauna and main threats (maritime traffic and floating marine litter), and involves several International partners that share common protocols for data collection across different routes in the Mediterranean Sea. This datasets includes 1432 georeferenced sightings of 8 cetacean species, together with effort data covered in good weather conditions (Beaufort <4), for a total of approximately 71.300 km, over 291 surveyed transects.