Two xanthones were isolated from the methanol extract of Garcinia cylindrocarpa stem wood found in Maluku Islands. Compound 1 had the lowest oxidation level compared to other xanthones found in G. cylindrocarpa and was a precursor to xanthone formation. Compound 2 showed stronger antimalarial activity against Plasmodium falciparum with an IC50 value of 0.12 μg/mL, compared to an IC50 of 4.67 μg/mL for compound 1. The isolation process and structure determination of the two compounds using spectroscopy methods are described.