A strain of Botrytis fabae isolated from faba bean (Vicia faba L.) plants displaying clear chocolate spot disease symptoms produced phytotoxic metabolites in vitro. The phytotoxins isolated from the culture filtrate organic extract were characterized by spectroscopic and optical methods. A new naphthalenone pentaketide, named botrytone, was isolated and characterized as (4R)-3,4-dihydro-4,5,8-trihydroxy-1(2H)-naphthalenone together with other well-known closely related naphthalenones such as regiolone and cis- and trans-3,4-dihydro-2,4,8-trihydroxynaphthalen-1(2H)-ones. When tested on leaves of the host plant, with the cis- and trans-3,4-dihydro-2,4,8-trihydroxynaphthalen-1(2H)-ones assayed in mixture, regiolone demonstrated the highest level of phytotoxicity together with cis- and trans-3,4-dihydro-2,4,8-trihydroxynaphthalen-1(2H)-ones. Botrytone showed moderate phytotoxic activity at 1 mg/mL and was still phytotoxic at 0.5 mg/mL.