The present study was conducted aiming to evaluate the in vitro and in vivo anti-parasitic efficacy of an isolated compound against the ciliate Cryptocaryon irritans. The compound was previously isolated from fermentation products of Streptomyces sp. CJK17 and designated as SFrD. Toxicity of the compound SFrD against the fish hosts (Larimichthys crocea) was also tested and its chemical structure was elucidated. The obtained results showed that the compound has potent anti-parasitic efficacy with the 10 min-, 1 h-, 2 h-, 3 h- and 4 h-LC50 (95% Confidence Intervals) of 6.8 (6.5–7.1), 3.9 (2.8–5.0), 3.3 (2.6–4.0), 2.7 (2.3–3.1) and 2.5 (2.2–2.8) mg L−1 against theronts of C. irritans and the 6 h-LC50 (95% CI) of 3.0 (2.8–3.2) mg L−1 against the tomonts, respectively. Exposure of the compound SFrD remarkably reduced the mortality of fish infected with C. Irritans, from 100% in the control group to 61.7% and 38.3% in groups of 3.1 mg L−1 and 6.3 mg L−1, respectively. In the test of exposing fish to 40 mg L−1 compound SFrD for 24 h, no visible effects were observed affecting the normal behavior or any macroscopic changes. By spectrum analysis (EI-MS, 1H NMR and 13C NMR), the compound SFrD was identified as Leptomycin B. This study firstly demonstrated that Leptomycin B has potent anti-parasitic efficacy against ciliates in cultured marine fish.