Uronema marinum, a well-known pathogenic parasite found in various marine fish species, caused severe economic losses in the field of aquaculture. This study aimed to assess the anti-parasitic activity and clarify the antiparasitic mechanism of active compounds isolated from the extracellular product of Salinivibrio proteolyticus strain YCSC6 against U. marinum in vitro. Two beta-carboline derivatives (beta Cs), harmane and norharmane, were isolated from the extracellular product of strain YCSC6 through the bioassay-guided fractionation. According to the results, harmane could eliminate U. marinum at 6 mg L-1 after 48 h exposure or 12 mg L-1 after 4 h exposure. Conversely, norharmane could eliminate U. marinum at 14 mg L-1 after 48 h exposure or 38 mg L-1 after 4 h exposure. The median effective concentration (EC50) of harmane after 4, 8, 12, 24 and 48 h exposure was 5.51 +/- 0.21, 3.63 +/- 0.08, 3.53 +/- 0.25, 2.87 +/- 0.12 and 2.47 +/- 0.12 mg L-1, and that of norharmane was 24.44 +/- 0.10, 16.63 +/- 0.14, 13.24 +/- 0.11, 6.50 +/- 0.02 and 4.53 +/- 0.15 mg L-1, respectively. In the aspect of anti-parasitic mechanism, harmane and norharmane transferred the electrons of 2-N to ground-state oxygen forming excessive reactive oxygen species (ROS), which damaged the plasma membrane and DNA of U. marinum. Meanwhile, the structure-activity relationship (SAR) analysis indicated 2-N was the necessary site for beta Cs to exert antiparasitic activity and the 1-methyl substitution could enhance the anti-parasitic activity. Our findings indicated that harmane and norharmane could be considered as promising lead compounds for developing novel and highly-effective anti-parasitic agents for aquaculture.