Phenotype is encoded in the genome in an indirect manner: each morphological structure is the product of many interacting genes, and most regulatory genes have several distinct developmental roles and phenotypic consequences. The lack of a simple and consistent relationship between homologous genes and structures has important implications for understanding correlations between evolutionary changes at different levels of biological organization. Data from a variety of organisms are beginning to provide intriguing glimpses of the complex evolutionary relationship between genotype and phenotype. Much attention has been devoted to remarkably conserved relationships between homologous genes and structures. However, there is increasing evidence that several kinds of evolutionary dissociations can evolve between genotype and phenotype, some of which are quite unexpected. The existence of these dissocations limits the degree to which it is possible make inferences about the homology of structures based solely on the expression of homologous genes.