This dataset gathers, total abundance, abundance per size class, total biomass and biomass per size class of two vulnerable fish species, the dusky grouper, Epinephelus marginatus (Lowe, 1834), and the brown meagre, Sciaena umbra Linaeus, 1758, recorded inside and outside the Marine Natural Reserve of Scandola (Corsica, NW Mediterranean) in 2012 and 2018. Fish were recorded by underwater visual censuses performed on belt transects (50 x 15 m) run parallel to the coast between 1 and 40 m depth at 13 sites according to three levels of protection status (integral reserve, buffer zone and unprotected zone). A total of 532 transects were performed in 2012 and 526 in 2018.