9-Hydroxy-3-methoxy-6H-pyrido[1,2-a]pyrazin-6-one, a new pyrido[1,2-a]pyrazine alkaloid named xylogranatinin, was isolated from the fruit of a Chinese mangrove Xylocarpus granatum. Its structure was elucidated on the basis of spectroscopic data, especially 2D NMR techniques including HSQC and HMBC. To the best of our knowledge, this is the first time that a pyrido[1,2-a]pyrazine alkaloid was found as a natural product.