<jats:title>Abstract</jats:title><jats:p>A novel metabolite xylopyridine A (<jats:bold>1</jats:bold>), together with a known compound pyrocoll (<jats:bold>2</jats:bold>), was isolated from mangrove endophytic fungus <jats:italic>Xylaria </jats:italic>sp. (#2508) collected from the South China Sea coast. Their structures were established on the basis of spectroscopic analysis, especially 2D‐NMR. Their affinities toward calf thymus (CT) DNA were studied by fluorescence quenching and spectrophotometric titration experiments. The results indicate that <jats:bold>1</jats:bold> showes strong DNA‐binding affinity presumably via an intercalation mechanism, thus it is exploitable as strong DNA‐binders.