DNA is packaged in the nucleus by winding it around histone proteins to form chromatin. The tails of histone proteins can be covalently modified at a number of specific sites. Specific modifications are associated with open, active chromatin (e.g. acetylations) and others with closed repressed chromatin (e.g. H3K9 methylations). Others are specific to promoters (H3K4me3) or other genomic features (e.g. enhancers). These modifications are often found in specific combinations that can be used to define chromatin states. The genome-wide chromatin state landscape, the epigenome, defines the biological state of a cell. We mapped chromatin states genome-wide in the O. dioica ovary and testis using 19 different histone modifications. We also profiled RNApolII, p300 and CTCF. Our data revealed sex-specific chromatin states, including a state specific to the Y-chromosome that may play a role in regulating the transcription of transposable elements. We also found marks typical of transgenerational inheritance as well as putative enhancer regions. Our work provides the first comprehensive view of a protochordate epigenome. We are now mapping the epigenome of the O. dioica embryo and are investigating the 3D organisation of the genome.