The role of TEs in genome size variation which accompanies adaptive and diversification processes in plants is explored. For this purpose, particular attention is focused on comparative genomic analyses of closely related species of ecological and agronomical interest from genus Lupinus (Fabaceae), which are adapted to contrasted ecological conditions and have remarkable genome size differences. Based on molecular cytogenetics and transposon-display approaches, our studies, not only revealed a high diversity of retrotransposons of ancient and recent origins, but also showed differential-lineage specific amplification of TEs among the Mediterranean and African lupines. Using high-throughput sequence data generated by NGS technologies, a first evaluation of the repeat compartment has been performed on the nuclear genome of Lupinus using similarity graph-based clustering and sequence characterisation methods. The results presented here allowed a most accurate identification and estimation of various families and subfamilies of TEs (mainly gypsy and copia elements), and other classes of repetitive DNA, in the genome of L. luteus, the biggest among the Old World lupins.