HIV-1 Integrase is a critical enzyme for replication of HIV, and its inhibition is one of the most promising new drug targets for anti-retroviral therapy with potentially significant advantages over existing therapies. Xanthoviridicatins E (1) and F (2) are two novel polyketide natural products that were isolated from a fermentation broth of an endophytic strain of Penicillium chrysogenum isolated from the living leaves collected in Peru. These compounds are new members of the unsymmetrical xanthoviridicatin family represented by the broader xanthomegnin family. Xanthoviridicatins E and F inhibited the cleavage reaction of HIV-1 integrase with an IC50 of 6 and 5 μM, respectively. The bioassay-directed isolation, structure elucidation, and HIV-1 inhibitory activity of these compounds are described.