These are exciting times for speciation research with a wealth of recent theoretical and empirical advances, but there is much we still do not understand. The Heliconius butterflies offer an excellent opportunity to gain novel insights into the genetic architecture of speciation and its genomic consequences, by integrating genomic data with the well-studied ecological and behavioural processes that underlie speciation in this group. Here I will bring together two lines of recent research in speciation, a) the evolution of genetic architectures, such as clustering of barrier genes, that facilitate divergence in the face of gene flow and b) the genomic patterns of divergence. First, I will apply large-scale whole genome resequencing to study divergence and gene flow between species, and test whether speciation proceeds through divergence of gradually expanding genomic islands under divergent selection. I will also develop novel theory to interpret these patterns. Second, I will test whether loci controlling behavioural and ecological traits that cause reproductive isolation are clustered in the genome, using a genome-wide quantitative trait analysis of reproductive isolation in two hybridizing species pairs. Third, I will investigate the role of chromosomal rearrangements in reducing between-species recombination rate where species hybridize, and directly study their influence on recombination rate. Overall, the project will integrate information on the distribution of genes controlling ecological, behavioural and genetic differences between species with patterns of recombination, in order to understand the process of genome divergence and adaptive radiation. This work will offer new insights into speciation, a process fundamental to evolution and biodiversity, but also has wider implications for our understanding of the processes that drive genome evolution.