These GBS data are from 169 clones of the rotifer Brachionus plicatilis. These clones derived from six experimental laboratory populations subjected to two contrasing selective regimes (predictable vs. upredictable). The set of clones were isolated after seven cycles of selection, and then, they were sequenced using genotyping by sequencing technique in order to elucidate the genomic basis of adaptation to unpredictable environments.