Large-scale chromosomal rearrangements may act as reproductive barriers, contributing to speciation. It has been hypothesised that chromosomal rearrangements are caused by repetitive elements such as transposons. Lepidoptera, i.e. butterflies and moths, which are among the most diverse groups across the Tree of Life, have holocentric chromosomes without defined centromeres. Chromosomal fusions and fissions are thought to be less deleterious in holocentric organisms and therefore more likely to be retained. Accordingly, some butterfly clades show a tremendous diversity of chromosome numbers. These clades often show bursts of species diversity, suggesting a role of rearrangements in speciation. To advance our understanding on the importance of repetitive elements and chromosomal rearrangements in speciation, we have generated and compared chromosome-scale genome assemblies for Erebia butterflies with differing chromosome numbers. We found support for a role of some repetitive elements in chromosomal rearrangements. Therefore, differences in repeat expansions might explain why some clades show a greater variation in chromosome numbers and a greater species diversity than others. Overall, we are disentangling the association between repetitive elements, chromosomal rearrangements, and species diversification in holocentric organisms.