Litchi dark pericarp disease (DPD) is a physiological disorder caused by manganese (Mn) stress and characterized by dark brown spots on the pericarp. The unknown pigments in the dark spots have hindered the progress in understanding its underlying mechanisms. In this study, we successfully isolated and identified four highly abundant and browning-prone light-colored litchidiols, six litchidiones (the oxides of litchidiols) and five dark dimers of litchidiols. Among these, 13 were first reported compounds. Further, litchidiol dimers were the dominant components of dark materials in the dark spots of diseased fruits, as supported by the dynamic conversions of these compounds in pericarp with the progression of DPD in field condition. In vitro synthesis experiments simulating dimer formation confirmed the concurrent participation of both litchidiol and litchidione compounds in the dimerization process. These findings first demonstrate the identity of ingredients in dark pericarp, and facilitate to further reveal the biochemical processes driving the formation of dark components in litchi under Mn toxicity.