Australian rock-wallabies have extensive chromosomal rearrangements across the genus (Petrogale). Chromosomal rearrangements are known to cause recombination suppression in the genome and thus create reproductive barriers and drive speciation. Whether this is a cause or consequence is often difficult to decipher. Using a targeted exon capture approach, we resolve the phylogenetic relationships across Petrogale to understand how chromosomal variation has evolved within this genus. In addition, we focus more detailed sampling across three parapatric species from Queensland to understand the links between chromosomal rearrangements, gene flow and speciation. Recent results indicate high levels of gene flow despite complex chromosomal rearrangements. We explore how gene flow patterns may change across the genome in relation to chromosome rearrangements. This is an exciting Australian system to explore the relationship between genome divergence and chromosomal rearrangements in speciation.