<p>The Zebrafish Anatomy Ontology (ZFA) is an application ontology used by ZFIN to support curation of expression and phenotype. The research community also uses the ontology to support annotation of high throughput studies. As the research focus of the zebrafish community evolves it drives changes in the ZFA. Here we provide an update on the changes made to support research carried out in adult fish and describe the changes in modeling of the neural crest in the ontology in order to bring the structure of the ontology into closer accordance with the morphological changes that occur during development.</p>