This are the data and R scripts used for the article "Genotyping-by-Sequencing and Morphology Revealed the Role of Polyploidization and Hybridization in the Diversification of the Centaurea aspera L. Complex of Section Seridia (Juss.) DC. (Asteraceae)" DOI: https://doi.org/10.3390/plants11151919. In the Western Mediterranean section, Seridia studies are scarce. In this section, Centaurea aspera forms a complex including four European diploid and one Moroccan autotetraploid subspecies, an allopolyploid, and hybrids among them. Here, we aimed to delimit the different taxa, identify any introgressions, and discuss their evolutionary history. Samples of all taxa were analysed using 1688 SNPs obtained through GBS and were morphologically characterized. Three genetically well-differentiated clusters were observed, corresponding to the allopolyploid C. seridis, the diploid C. aspera and the cryptic autotetraploid C. aspera ssp. gentilii, which is proposed to be considered as a species. Centaurea seridis showed a high isolation by distance, a greater morphological variability, and a lack of interspecific gene flow. Diploid and autotetraploid C. aspera individuals were morphologically similar, and some introgressions were detected in Southern Spain, where new forms may promote diversification. This gene flow might have taken place during the Messinian and before autopolyploidization occurred in Morocco. In the C. aspera complex, current interspecific barriers are strong, while polyploidization may provide a better adaptation to drier environments.