The 12th European Conference on Fungal Genetics (ECFG) was held in Seville, Spain on March 23-27, 2014. The meeting covered topics as diverse as fungal genetics, genomics, molecular cell biology, evolution, pathogenesis, and biotechnology. Despite such diversity, as the meeting progressed, it became evident that epigenetics are now an important part of genomic studies on fungal biology and evolution. In the meeting, regulation of genome integrity, secondary metabolism gene cluster and light responses by histone modifications and also small RNA-mediated antifungal drug resistance were reported. In this report, we highlight those epigenetics-related talks presented in the 12th ECFG that give new insights into the biology and evolution of microbial eukaryotes.