Objective: To explore the effects of peptides derived from Spirulina protein hydrolyzed by alkali protease on mucosal immune system in rabbits. Methods: Protein was extracted from Spirulina by salting out method, and then hydrolyzed with alkaline protease. The rabbits were treated with the hydrolysate by intragastric administration, intraperitoneal injection and ear vein injection, respectively. At 3, 2 and 2 h after administration, ELISA kit was used to determine the concentration changes of IL-1β, IL-6, IL-12, IFN-γ, TNF-α, IL-1Ra, IL-4, IL-10 and TGF-β in rabbit serum. Results: Compared with the control group treated with physiological saline, all the three administration route groups showed a notable decrease in the concentration of IL-12 but an increase in both the concentrations of IFN-γ and IL-10. However, on the basis of the comparison among the three administration routes, intraperitoneal injection revealed the most remarkable change in cytokines; in contrast, the two others had no obvious change. In the intraperitoneal injection group, the concentrations of IL-1 β, IL-6, IL-12 and TNF-α revealed a significant decrease, while those of IL-1Ra and IL-4 exhibited a dramatic increase, which suggests that the peptides derived from Spirulina protein hydrolyzed by alkali protease have strong immune activity. Conclusion: The immune signaling transduction of Spirulina peptides in mucosal immune system is completed by inhibiting NF-κB and PKC/p38/MAPK pathways in mucosal epithelium, endothelial cell, monocytes/macrophages and lymphocytes, which is similar to the phytochemical mechanism for inhibiting NF-κB and inflammatory reaction.