In eukaryotic cells, the genetic material is organized into chromatin, which consists mainly of DNA, histones and chromatin-associated proteins. An important regulator of chromatin structure and function are histone post-translational modifications, which can shape gene expression patterns and control the epigenetic landscape. Here, we summarize the role of some key histone modifications in animal development, with a focus on the two best-studied types of histone modifications: lysine methylation and acylations, specifically, acetylation.