While chromosomal rearrangements are ubiquitous in all domains of life, very little is known about their evolutionary significance, mostly because, apart from a few specifically studied and well-documented mechanisms (interaction with recombination, gene duplication, etc.), very few models take them into account. As a consequence, we lack a general theory to account for their direct and indirect contribution to evolution. In this thesis , we use forward-in-time simulation platforms and formal modeling to unraveling the evolutionary significance of chromosomal rearrangements. Despite being almost invisible in the phylogeny owing to the scarcity of their fixation in the lineages, we show that chromosomal rearrangements make a decisive contribution to the evolutionary dynamics. We also show that chromosomal rearrangements tightly regulate the size of the genome through indirect selection for reproductive robustness. Overall, our results provide a theoretical understanding of the contribution of chromosomal rearrangements to evolution.