Phytophthora spp are one of the most devastating pathogens to a wide range of crop plants. Chemical fungicides are commonly used for controlling Phytophthora diseases, however, due to environmental concerns and development of fungicide resistant Phytophthora strains, alternative low-risk method such as biological controls are the prospective approaches. In an in vitro bioactivity-driven screen of rhizosphere-inhabiting fungi, Aspergillus flavipes was identified as a strong inhibitor for growth of various species of Phytophthora. As well as, the crude extracellular extract of broth cultures of A. flavipes displayed a significant growth inhibition of various Phytophthora spp, with EC50 values ranged from 0.018−0.02 units. Bioactivity-driven fractionation analyses revealed that the antiphytophthoral activity was mostly reported in the ethyl acetate fraction. In addition to mycelial growth inhibition, the ethyl acetate fraction inhibited the zoospore germination and sporangial production in P. parasitica. Microscopic analyses of P. parasitica hyphae treated with A. flavipes ethyl acetate extract, revealed severe growth abnormalities such as irregular condensed hyphal aggregations, shorter hypha and thicker cells, in addition to the strongly inhibition of P. parasitica infection and pathogenicity to Nicotiana benthamiana. From the direct co-culturing, P. parasitica and its metabolites had no effect on over elicitation of the active metabolites of A. flavipes. The putative antiphytophthoral compounds from A. flavipes were chemically verified as 3-hydroxy-2′,4,4′,6′-tetramethoxychalocone, 7,3,4,5′-tetramethoxyflavanone, isovitexin and amodiaquine at concentrations 35.8, 9.1, 26.4 and 11.4%, respectively. The cultures of A. flavipes and its active extracts did not display any phytotoxicity to N. benthamiana and S. lycopersicum suggesting their potentially for controlling the diseases of Phytophthora spp.