There is growing evidence that non-genetic factors play an important role in animal diversification, from horn variation in beetles to eye loss in cavefish. “Epigenetics” describes modifications that alter DNA packaging, chromatin structure and thus gene expression. To investigate the role of epigenetic factors in species-specific diversification, we used Lake Malawi cichlids. These fishes underwent a textbook adaptive radiation and a hallmark of this is diverse craniofacial morphologies that define feeding mechanisms along a pelagic/benthic axis. To assess the phenotypic effect of altered epigenetic regulation, we inhibited histone deacetylation (HDACs) using the drug Trichostatin A (TSA) during specific windows of facial development in both zebrafish and three Malawi cichlid species with distinct adult morphologies (Tropheops sp. and Maylandia sp.). Results were quantified using geometric morphometric shape analysis. In both zebrafish and cichlids, we found that during neural crest cell migration, treatment with TSA significantly altered facial shape resulting in an overall wider Meckel’s cartilage, wider branchial structures and an overall shorter head (ZF: p=0.03 vs. controls; T.ch.: p=<0.001 vs. controls). In cichlids, there were species-specific effects in induced phenotypic variation. This may suggest that the regulation of HDACs is robust, but there may be other molecular architecture that influence phenotypic divergence and that some species may be more “evolvable” than others. TSA treatment during later timepoints showed no significant changes to craniofacial morphology in zebrafish or cichlids. This work shows that neural crest cell migration is a sensitive interval for HDACs to impact “normal” craniofacial development both in zebrafish and in cichlids. Epigenetic mechanisms may have a widespread role in morphological diversification across vertebrates.