In the present study, the apoptosis and tissue changes in the spleen, as well as humoral immune-related parameters, micronuclei (MN) induction in blood cells and Ethoxyresorufin-O-deethylase (EROD) activity were investigated in yellowfin seabream (Acanthopagrus latus) after short-term exposure to phenanthrene (Phe). The fish were intraperitoneally injected with different concentrations (2, 20 and 40 mg kg−1) of Phe and tissue and blood samples were collected 1, 4, 7 and 14 days after injection. The concentrations of Phe in the fish liver increased 4 days after the experiment. EROD activity showed a pattern consistent with Phe concentration in the liver. Apoptotic index in the spleen increased dose dependently in Phe-exposed fish. Exposure to Phe caused significant decrease in the plasma level of immunoglobulin M, phagocytic and respiratory burst activity after 4 days of exposure. The frequency of MN in the erythrocytes of the treated fish was significantly higher than control. The main pathological alterations in the spleen included the increase in melanomacrophage centers (MMCs), destroyed red blood cell and hemorrhage. The degree of tissue changes in the spleen of the exposed fish ranged from slight to moderate damage. The size and number of MMCs in the spleen were significantly higher in Phe-treated fish compared to the control. Our results showed that Phe could suppress immune responses in fish, induce cell apoptosis, histological changes in the spleen and MN formation. This may suggest those parameters consider as useful biomarkers for monitoring of the health status of fish during exposure to Phe.