Extracts from three Calophyllum species endemic to Sri Lanka were tested for antifungal and antioxidant activities. Of them, only the root methanol extract of Calophyllum thwaitesii showed activity, and the active extract on activity guided fractionation yielded four antifungal active and three inactive xanthones. Antifungal active xanthones were identified as 1,6-dihydroxy-5-methoxyxanthone, 1-hydroxy-5,6-dimethoxyxanthone, 1-hydroxy-5-methoxyxanthone and 1-methoxy-5-hydroxyxanthone, using spectroscopic methods and comparison with literature data. Inactive compounds were identified as 1-hydroxy-7-methoxyxanthone, 1,5-dihydroxy-6-methoxyxanthone and 1,7-dihydroxy xanthone. This is the first report of above xanthones except the latter from C. thwaitesii. Further, five of the above xanthones along with thwaitesixanthone and calothwaitesixanthone, which have been previously reported from the root bark of the same species, showed free radical scavenging properties when tested with DPPH. Further, this is the first report of methylated xanthones from C. thwaitesii. Previous work on stem bark, root bark and the stem of the same species yielded only nonmethylated xanthones, indicating the absence of methylating enzymes in the plant. However, this new finding suggests the presence of methylating enzymes in the root stem of C. thwaitesii.