Vaccination is an effective method for controlling bacterial and diseases of fish. At present, researchers have paid more attention to variations of immune related genes expression to evaluate the immune effect of vaccine, besides the changes of antibody level of serum and mucus, enzyme activity, number of lymphocytes, respiratory burst, complement activity and so on. The proinflammatory cytokines such as interleukin-1β (IL-1β), tumor necrosis factor α (TNF α) and chemokines are the key factors in inducing inflammatory and immune cell migration, immune regulation and stimulating the proliferation of T cells and B cells. Major histocompatibility complex class I (MHC I), major histocompatibility complex class II (MHC II), T cell surface receptor CD4, T cell surface receptor CD8 and immunoglobulin M (IgM) play key roles in different stages such as presentation and recognition of antigens and immune response after pathogens invasion. These factors finally to remove pathogens and maintain healthy through a series of immune response. Numerous studies have showed that the vaccine could cause rapid changes in many immune related genes. For purpose of studying the influence of immune methods of vaccine on expression of immune related genes, were injected intraperitoneal and immersed with inactivated vaccine respectively in this study. The expression of seven immune related genes, IL-1β, TNF α, MHC I, MHC II, CD4, CD8 and IgM in spleen, head kidney and gills was determined by quantitative real-time polymerase chain reaction (qRT-PCR) at 0 h, 4 h, 8 h, 12 h, 24 h, 48 h, 72 h, 96 h, 7 d and 14 d post immunization. The results showed that, the expression of all the tested genes varied significantly. In the injection group, the expression of IL-1 β and TNF α reached the peak between 12–24 h, and MHC I, MHC II, CD4 and CD8 occurred between 48–72 h and peak of IgM appeared at 7 d. The gene maximum expression was 2–70 times higher than that of control group. By contrast, in immersion group, the expression of IL-1 β and TNF α reached their peak between 12–48 h, and MHC I, MHC II, CD4 and CD8 occurred within 48–96 h. IgM peak appeared at 96 h in the gills, but 14 d later in spleen and head kidney, the maximum amount was 2–20 times higher than that in control. The results indicated that, the transcriptional level of genes in injection group was higher than that of immersion group in spleen and head kidney. In addition, the highest value appeared earlier in injection group than in immersion group. However, the gene expression peak in gills appeared later than immersion group. Data are referring for the evaluation of vaccine.