Bacterial blight, an important and potentially destructive bacterial disease in rice, is caused by Xanthomonas oryzae. Recently, this organism has developed resistance to available antibiotics, prompting scientists to find a suitable alternative. This study focused on secondary metabolites of Phomopsis longicolla to target X. oryzae. Five bioactive compounds were isolated by activity-guided fractionation from ethyl acetate extracts of mycelia and were identified by LC/MS and NMR spectroscopy as dicerandrol A, dicerandrol B, dicerandrol C, deacetylphomoxanthone B, and fusaristatin A. This is the first time fusaristatin A has been isolated from Phomopsis sp. Deacetylphomoxanthone B showed a higher antibacterial effect against X. oryzae KACC 10331 than the positive control (2,4-diacetyphloroglucinol). Dicerandrol A also showed high antimicrobial activity against Gram-positive bacteria (Staphylococcus aureus, Bacillus subtilis) and yeast (Candida albicans). In addition, high production yields of these compounds were obtained at the stationary and death phases.