The present research has investigated the effect of Lactobacillus farraginis (LF) and Enterococcus durans (ED), isolated from kefir, as probiotic on innate immune parameters and expression of IL-1β and TNF-1α lysozyme genes in the intestine, as well as resistance to the Lactococcosis in rainbow trout. Four hundred and eighty juveniles (41.9 ± 2.4 g) were divided into eight groups with three replications, including the control, LF1 and LF2 supplemented with 10 7 and 10 8 Cfu/g feed of each strain, Bactocell equivalent to 10 10 , ED1 and ED2 with 10 7 and 10 8 Cfu/g feed of each strain, combination supplements LF1+ED1 and LF2+ED2 with 5 × 10 6 and 5 × 10 7 Cfu/g feed of each strain. Compared to control, a significant increase (p < 0.05) was observed in in serum lysozyme, ACH50, C3 and C4, total antibody, bactericidal activities and blood phagocytosis in LF2, Bactocell, LF2+ED2, and ED2 treatments. Besides, lysozyme gene expression in the intestinal tissue of fish treated with LF2, ED2, and Bactocell significantly increased (p < 0.05). A significant increase in TNF-1α gene expression was also observed in all treatments except LF1 and ED1 (p < 0.05). Moreover, a significant increase in the level of IL-1β gene expression was observed in all groups, except for ED1 and LF1+ED1, in comparison to the control treatment. After challenge with Lactococcus garvieae, the lowest mortality percentages were recorded for LF2, Bactocell, LF2+ED2, and ED2 treatment compared to the control. The results suggest beneficial effects of kefir derived LAB strains on immune responses, immune-related genes expression, and disease resistance in rainbow trout.