A central goal of evolutionary biology is to understand the genetic origin of 
morphological novelties-i.e. anatomical structures unique to a taxonomic group. 
Elaboration of morphology during development depends on networks of regulatory 
genes that activate patterned gene expression through transcriptional enhancer 
regions. We summarize recent case studies and genome-wide investigations that 
have uncovered diverse mechanisms though which new enhancers arise. We also 
discuss how these enhancer-originating mechanisms have clarified the history of 
genetic networks underlying diversification of genital structures in flies, 
limbs and neural crest in chordates, and plant leaves. These studies have 
identified enhancers that were pivotal for morphological divergence and 
highlighted how novel genetic networks shaping form emerged from pre-existing 
ones.