27 endophytic fungi were isolated from the barks and fruits of Camptotheca acuminate and then cultured in submerged fermentation. The fermentation products of each strain were analyzed with high performance liquid chromatography (HPLC) which showed that one produced camptothecin with the output of 774 μg/L. The strain was identified as Phomopsis sp. by phylogenetic analysis based on ITS rDNA and cultural and morphological characteristics. This was the first report that Phomopsis sp., which was isolated from Camptotheca acuminate, produced camptothecin.