Previous studies proposed extensive chromosomal rearrangements among Lens species, with implications for both breeding and evolutionary genomics. We used wet-lab and bioinformatics approaches to explain why and where those rearrangements are happening during Lens spp. evolution. The genomes of each of the seven species were assembled. Gene synteny analysis was performed, and centromeres were localized using CenH3 ChIP-Seq experiments to investigate the involvement of centromeres in chromosomal stability. An oligo-FISH (Fluorescent in situ hybridization) system was developed to confirm in situ the rearrangements detected through the synteny analysis, and the complete and comparative characterization of the satellite DNA genome fraction of all Lens species was performed. The telomeres and ribosomal DNA sequences were located across the cultivated L. culinaris chromosomes, aiming to check for any variation that could be associated with the chromosomal changes.