The establishment and inheritance of individualized structural units is a key feature of morphological evolution, embodied in the concept of homology. In current debates, homology is often equated with identical genetic encoding. The empirical evidence for this assumption is ambiguous. Genetic identity can indicate morphological identity in some cases, but several examples show that gene expression patterns and regulatory systems of development may be highly conserved while morphological characters undergo dramatic evolutionary innovation. This indicates some independence of structural homology from its genetic and developmental makeup. It is proposed that phenotypic evolution depends strongly on the epigenetic context in which genetic redundancy becomes available for the control of new developmental interactions. The integrated character of developmental systems may represent an important factor in the origin and identity of morphological characters and can stabilize incipient structures before their full genetic integration. The origin of the autopod section of the tetrapod limb is an example which suggests that novel homologues can arise in evolution as a consequence of changing the epigenetic context of conserved gene function.