Plant pathogens secrete an arsenal of small secreted proteins (SSPs) acting as effectors that modulate host immunity to facilitate infection. In fungi, SSP-encoding genes are often located in particular genomic environments and show waves of concerted expression during plant infection. To date, little is known about the regulation of their expression. Leptosphaeria maculans, a fungus responsible for stem canker of oilseed rape, has a bipartite genome structure alternating gene-rich and transposable element (TE)-rich regions. TE-rich regions, which encompass one third of the genome, are enriched in putative effector genes that present the same expression pattern (no or a low expression level during in vitro growth and a strong over-expression in planta). On these bases, we investigated the determinism of the concerted effector gene expression testing two hypotheses: (i) are one or several common regulators involved in the control of the concerted expression of effector genes? and / or (ii) are TE-rich regions targets of reversible chromatin modifications that affect the regulation of effector gene expression? To identify putative regulators of effector gene expression, we established the repertoire of TFs of L. maculans and identified TFs only found in L. maculans genome or specifically induced during infection. We performed functional analyses on several TFs and showed that StuA plays a major role in infection and expression of effector genes in L. maculans. We also investigated the involvement of one histone modification, histone H3 lysine 9 tri-methylation (H3K9me3) in chromatin-based regulation of concerted effector gene expression. For this purpose, we silenced expression of two key players in heterochromatin assembly and maintenance, HP1 and Kmt1, by RNAi. Whole genome oligoarrays performed on silenced-HP1 and silenced-Kmt1 transformants revealed an over-expression of SSPencoding genes in TE-rich regions during in vitro growth. That increase of expression was associated with a reduction of H3K9 tri-methylation at two SSP-encoding gene loci. These data strongly suggest that a chromatin-based control, mediated by HP1 and KMT1, represses the expression of at least part of the effector genes located in TE-rich regions during growth in axenic culture. Our hypothesis is that changes of lifestyle and a switch toward pathogenesis lift chromatin-mediated repression, allowing a concerted expression of effector genes mediated by one / or several TF(s).