We searched for bioactive substances involved in flower bud formation of Arabidopsis thaliana. Some significantly decreasing HPLC peaks were detected in the extract of flower buds-forming A. thaliana compared with that of the non-flower bud-forming stage. Compound 1, which corresponded to the most decreased HPLC peak, was isolated from aerial parts of A. thaliana. From NMR and MS data, compound 1 was identified as one of the monogalactosyl diacylglyceride (MGDG). Compound 1 induced flower bud formation of A. thaliana exposed to long day condition for only 1 day. These results suggest that compound 1 as a precursor or a substrate of flower bud-forming substances plays important roles in the flower bud formation of A. thaliana.