The goal of the study aimed at understanding better how secondary metabolite biosynthetic gene clusters (BGCs) are regulated by histone post-translational modifications (PTMs). Gene expression of secondary metabolite BGCs, and BUSCO genes as control, in young mycelium of Aspergillus fumigatus Af293, Aspergillus nidulans pabaA1 and Aspergillus niger NRRL3 was correlated to histone PTMs and genomic localization. This study is relevant for the activation of silent BGCs and discovery of novel bioactive molecules produced by fungi.