Metabolism and in vitro fungitoxicity of perinaphthenone against three economically important fungi of the citrus, Botryodiplodia spp., Botrytis spp. and Fusarium spp. were investigated. Perinaphthenone exhibited significant antifungal activity at 62.5 μM and above. Even, the inhibitory effect against Fusarium spp. was significantly enhanced by exposure to direct light. In addition, the metabolism of perinaphthenone by the three fungi was studied. Results show that perinaphthenone was transformed almost completely during the first 24 h; two major products, whose concentration increased progressively during the twelve days of the test, were isolated and identified as 2,3-dihydro-1H-phenalen-1-ol and 2,3-dihydro-phenalen-1-one. Although both metabolic products displayed a considerable fungistatic effect, their slightly lower activities in comparison to perinaphthenone indicate that the transformation was a detoxification process. Studies on the relationship between the effect of some substituents in the perinaphthenone core and the mycelial growth inhibition of Botryodiplodia spp. were also carried out. Results show that the α, β-unsaturated carbonyl system is an important structural requirement but not the only to be necessary for the strong antifungal activity of perinaphthenone. In general, the antifungal properties of perinaphthenone may be modulated through the incorporation of substituents in the naphthalene core or in the α, β-unsaturated carbonyl system. It is concluded that perinaphthenone could be used as an antifungal agent or as a structural template for the development of new fungicide compounds.