Leptosphaeria maculans, a hemibiotrophic fungus responsible for stem canker, colonises oilseed rape in two stages: an early stage of cotyledon or leaf colonisation, and a late colonisation stage during which the fungus colonises systemically without visible symptom the plant before stem canker appears. L. maculans presents a bipartite genome structure alternating gene-rich and transposable element (TE)-rich regions. While TE-rich regions are enriched in putative effectorencoding genes strongly over-expressed during early infection ('early' effectors), gene-rich regions contain putative effector-encoding genes specifically expressed during late infection ('late' effectors). Here, we analyzed nucleosome positioning, chromatin structure and gene expression at the genome scale combining MAINE-seq, ChIP-seq and RNA-seq data during axenic growth and performed functional analysis of two players of heterochromatin assembly (KMT1 and KMT6). We analyzed in vitro ChIP-seq data targeting two heterochromatin modifications, H3K9me3 and H3K27me3, and a euchromatin modification, H3K4me2, and found that gene-rich regions are associated with H3K4me2 and H3K27me3 while TE-rich regions are associated with H3K9me3. Analysis of in vitro MAINE-seq data showed distinct nucleosome organization for genes located in TE-rich or gene-rich regions, and according to gene expression level. CRISPR-Cas9 mutants of KMT1 and KMT6 have been generated and are currently characterized for their ability to infect leaves and stems of oilseed rape, and to express effector genes.