During gametogenesis and embryonic development, precise regulation of gene expression, across cell/tissue types and over time, is crucial. In vertebrates, transcription is partly regulated by histone lysine acetylation/deacetylation, an epigenetic mechanism mediated by lysine acetyltransferases (KAT) and histone deacetylases (HDAC). Well characterized in mammals, these enzymes are unknown in fish embryology outside of zebrafish development. Here, we characterized putative KAT and HDAC enzymes in the self-fertilizing mangrove rivulus fish, Kryptolebias marmoratus, a species that naturally self-fertilizes and can produce isogenic lineages. This unique feature provides an opportunity to elucidate the role of epigenetic mechanisms as a source of phenotypic plasticity. In this study, twenty-seven KAT and seventeen HDAC genes have been identified. Their conserved domains and their phylogenetic analysis suggest conservation of the enzymes' activity in our species, relative to other vertebrates in which the enzymes have been characterized. Furthermore, the dynamics of KAT and HDAC mRNA expression during embryogenesis, in adult gonads and brains, argues for a putative biological function in early and late development as well as in male/hermaphrodite gametogenesis and adult neurogenesis. Our study aimed to provide a basis about the epigenetic actors putatively regulating histone acetylation in a self-fertilizing fish, the mangrove rivulus. Unique among vertebrates, the great number of isogenic lineages occurring naturally in this species allows exploring the contribution of the enzymes regulating histone acetylation only to reproduction and development in teleost fishes, which are very powerful models in fundamental and applied researches that include aquaculture, ecotoxicology, behaviour, evolution, sexual determinism and human diseases.