An important goal in evolutionary biology is to understand the genetic changes underlying novel morphological structures. I discuss the origins of complex wing patterns found among neotropical Heliconius butterflies. Genome sequence data from 100s of individuals across two major radiations has identified narrow regions associated with distinct colour pattern elements. We hypothesise that these modules in non-coding sequence represent distinct cis-regulatory loci that control expression of just 3-4 key genes, including the transcription factor optix and the morphogen WntA, which in turn control pattern variation across Heliconius. Phylogenetic analysis of these elements demonstrated that they have distinct evolutionary histories and that novel adaptive morphological variation was created by shuffling these cis-regulatory modules through recombination between divergent lineages. In addition, recombination of modules into different combinations within species further contributes to diversity. Analysis of the timing of diversification supports the hypothesis of introgression moving regulatory modules between species, rather than shared ancestral variation, as divergence can be much younger at wing pattern loci relative to species divergence. I therefore argue that shuffling of existing enhancer elements both within and between species provides a mechanism for rapid diversification and generation of novel morphological combinations during adaptive radiation