In recent years, marine-derived Penicillium fungi have received remarkable interest as a valuable source of novel natural products encompassing diverse chemical structures and bioactive properties. Mangroves, sediments, algae, and sponges are the four main sources of marine-derived Penicillium fungi. As of 2014, more than 390 novel natural products have been isolated from the marine-derived Penicillium fungi, mainly including polyketides, alkaloids, terpenoids, and macrolides. Biological investigations have shown that these compounds possess antimicrobial, anti-inflammatory, cytotoxic, and other activities with potential applications in new drug development. To provide an updated catalog of this field, our mini-review summarized the origins, structures, and bioactivities of 188 secondary metabolites from marine-derived Penicillium fungi based on bioactivities classification published from 2015 to 2020.