Belgian microbiologist Philibert Melchior Joseph Ehi Biourge was the first to describe P. rubens in 1923. The medicinal importance was discovered by Alexander Fleming, a physician at St Marys Hospital, London. In September 1928, Fleming found that one of his bacterial cultures (of Staphylococcus aureus) was contaminated with mould, and that the area around the mould inhibited bacterial growth. He gave the name penicillin for the purported antibacterial substance produced by the mould. After a series of experimental tests, he published his discovery in the June 1929 issue of the British Journal of Experimental Pathology. With the help of his colleague Charles J. La Touche, Fleming identified the fungus as Penicillium rubrum'.
But Charles Thom at the U. S. Department of Agriculture, Peoria, Illinois, compared the specimen with his collection of Penicillium species, and corrected the species as P. notatum. In his publication in 1931, he resolved that P. notatum was a member of P. chrysogenum species complex, which he had described in 1910. P. notatum was described by Swedish chemist Richard Westling in 1811. Thom adopted and popularised the use of P. chrysogenum. After discovery of other new species and taxonomic reexamination, three species, P. notatum, P. meleagrinum, and P. cyaneofulvum were recognised as P. chrysogenum. The Seventeenth International Botanical Congress held in Vienna, Austria, in 2005 adopted the name P. chrysogenum as the conserved name (nomen conservandum).
Whole genome sequence and phylogenetic analysis, particularly using β-tubulin sequences, in 2011 showed that P. notatum is P. rubens, and that P. chrysogenum is a different species.