The gibbons (family Hylobatidae) occupy a key node in the primate phylogenetic tree. They are characterised by an accelerated rate of evolutionary chromosomal rearrangements. To date, despite much effort, the phylogeny of gibbons remains largely unresolved at the genus level, likely due to rapid divergence of the four genera approximately 5 million years ago. In this chapter we discuss various approaches used to untangle the complex phylogeny of the gibbons. We highlight the unique branching pattern of the gibbon tree, which suggests that the four genera diverged over short evolutionary time. Furthermore, we review how cutting-edge DNA sequencing technologies have improved our understanding of the evolution of the gibbon genome and how this can guide conservation efforts. In particular, we describe the mechanisms that have contributed to the highly rearranged karyotypes of the gibbon genera and how the birth and consequent propagation of the gibbon-specific transposable element LAVA might have shaped the evolution of this lineage by inserting within nearby genes involved in chromosome segregation and DNA repair. As more genetic resources and data are generated from gibbon species, we will gain further insight into the evolutionary history and enable progress towards generating greater infrastructures to conserve these threatened species.