The study explored the possibility of using intron regions as a source of quantifiable variability and applying them to Molecular Ecology studies of non-model organisms (species identification and population genomics). Introns have the advantage that they can be highly variable in sequence but their position, as well as their exon-flanking regions, are often conserved easing the selection of intron markers potentially highly transferable between species of the same taxonomic group. This intuition proved to be correct and after the development of an optimized procedure for i) the isolation of panel of loci highly transferable across species, ii) the simultaneous genotyping of hundreds of introns in hundreds of individuals through Illumina sequencing and iii) the post processing of raw data through a dedicated bioinformatic approach, we propose the Multi-locus Intron Polymorphisms (MIPs) as an alternative category of molecular markers for the analyses of genetic diversity in non-model organisms at different diversity levels. This BioProject includes raw sequencing data of the first 121 intronic loci obtained from 65 species of Teleost fishes. These data were analysed as described in the related paper.