Investigation of the chemical constituent and antibacterial activity of Diaporthe amygdali SgKB4, an endophytic fungal strain isolated from the West Sumatran mangrove plant Sonneratiagriffithii Kurz led to the isolation of compound 1. The isolation of compound 1 was achieved by column chromatography with step gradient polarity (SGP) method and purification by recrystallization. The structure of compound 1 was elucidated based on nuclear magnetic resonance (NMR) spectroscopy data. Based on IR, 1D, and 2D-NMR, as well as MS data, the isolated compound is cytochalasin H. This compound showed mild antibacterial activity against some pathogenic bacteria. This is the first report on the isolation of cytochalasin H from the endophytic fungus D. amygdali.