[3] Molecular phylogeny has established that Alexander Fleming's first discovered penicillin producing strain is of a distinct species, P. rubens, and not of P.

Other secondary metabolites of P. chrysogenum include roquefortine C, meleagrin,[7] chrysogine,[8] 6-MSA[9] YWA1/melanin,[10] andrastatin A,[11] fungisporin,[12] secalonic acids, sorbicillin,[13][14] and PR-toxin.

[15] Like the many other species of the genus Penicillium, P. chrysogenum usually reproduces by forming dry chains of spores (or conidia) from brush-shaped conidiophores.

Observations of morphology and microscopic features are needed to confirm its identity and DNA sequencing is essential to distinguish it from closely related species such as P. rubens.

The ability to produce penicillin appears to have evolved over millions of years, and is shared with several other related fungi.

The principal genes responsible for producing penicillin, pcbAB, pcbC, and penDE are closely linked, forming a cluster on chromosome I.