A diverse range of farmed and wild Mediterranean populations of the European seabass (n = 24) and the gilthead seabream (n = 27) were collected for SNP discovery. Population pools were prepared by combining the DNA of 25 different individuals. For the majority of sampled populations, pools were prepared in duplicate (technical replicates). For a few populations (6 and 3 populations in the European seabass and gilthead seabream, respectively), a single population pool was prepared. Details of the origin of the populations used for DNA pooling can be found in the publication associated with this study.