Azaphilones have continuously aroused considerable attention owing to their structural diversity and significant biological activities recently. This review attempts to give a comprehensive summary of recent progress on the isolation, identification, and biological activity, along with synthetic and biosynthetic studies of azaphilones reported from October 2012 to December 2019. Herein, a total of 252 compounds predominantly originated from 32 genera of fungi, such as Penicillium (20%) and Talaromyces (11%), were included in this research with citations of 105 references. Among these azaphilones, approximately half of them were found with various biological activities, of which over 40% displayed cytotoxic/anti-tumor effects. This review would shed light on the future development and research of azaphilones.