The revolutionary discovery of penicillin only marks the start of our exploration for valuable fungal natural products. Advanced genome sequencing technologies have translated the fungal genome into a huge reservoir of “recipes” – biosynthetic gene clusters (BGCs) – for biosynthesis. Studying complex fungal genetics demands specific gene manipulation strategies. This review summarizes the current progress in efficient gene targeting in fungal cells and heterologous expression systems for expressing fungal BGCs of fungal secondary metabolites.