The establishment and inheritance of individualized structural units i
s a key feature of morphological evolution, embodied in the concept of
homology. In current debates, homology is often equated with identica
l genetic encoding. The empirical evidence for this assumption is ambi
guous. Genetic identity can indicate morphological identity in some ca
ses, but several examples show that gene expression patterns and regul
atory systems of development may be highly conserved while morphologic
al characters undergo dramatic evolutionary innovation. This indicates
some independence of structural homology from its genetic and develop
mental makeup. It is proposed that phenotypic evolution depends strong
ly on the epigenetic context in which genetic redundancy becomes avail
able 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 stabili
ze incipient structures before their full genetic integration, The ori
gin of the autopod section of the tetrapod limb is an example which su
ggests that novel homologues can arise in evolution as a consequence o
f changing the epigenetic context of conserved gene function.