Propolis is a resinous substance collected by honeybees from various plant sources. The composition of propolis depends upon the vegetation at the site of collection. We previously isolated four prenylated flavonoids from propolis collected in Okinawa, Japan. In this study, further fractionation of the extracts of Okinawan propolis resulted in the isolation of a new prenylated flavonoid, prokinawan, and four known compounds. The structure of prokinawan was determined by MS and NMR spectroscopic methods. Furthermore, the antioxidant activity using 1,1-diphenyl-2-picryl-hydrazyl radical scavenging and beta-carotene bleaching systems was investigated. The present study proved that the position of the geranyl or prenyl groups on the flavonoid skeleton plays an important role in exhibiting antioxidant activity.