Abstract
Advances in multiple disciplines such as genetics, molecular biology, and organismal biology have highlighted the importance of epigenetic marks in gene regulation, development, and adaptation. The growing interest in this area has led to the development of a large number of analytical methods and tools to study the epigenome. These techniques allow the characterization and quantitation of epigenetic modifications, including cytosine methylation, histone modifications, and noncoding RNA. With the plethora of options available, choosing the best‐suited strategy becomes challenging. This chapter aims to summarize current methods to analyze the epigenome and provide the reader with informative elements regarding strategy selection. Furthermore, bioinformatics analysis tools and resources are presented, providing a wider picture of the possibilities and limitations of these approaches. We expect this chapter to provide a framework for epigenomic analysis that is useful in aquaculture, and more broadly, to the scientific community.