GAP-43 (a.k.a. B-50, F1, pp46, or neuromodulin) is a major growth cone membrane protein whose expression is widely correlated with successful axon elongation, but whose function remains unknown. To distinguish the structural features of GAP-43 most relevant to its cellular functions, we have determined features of the protein that are most highly conserved in vertebrate evolution. Comparison of fish and mammalian GAP-43 distinguishes two domains of the protein. A strictly conserved amino-terminal domain contains the putative site for fatty acylation and membrane attachment, a calmodulin binding domain, and a proposed phosphorylation site. In the much larger carboxy-terminal domain, amino acid composition is strongly conserved without extensive sequence conservation. This amino acid composition predicts an extended, negatively charged rod conformation with some similarity to the side arms of neurofilaments. The results suggest that the biological roles of GAP-43 may depend on an ability to form a dynamic membrane-cytoskeleton-calmodulin complex.