The endocannabinoid system plays an important role in regulating inflammation in several chronic or anomalous gut inflammatory diseases. In vivo and ex vivo studies showed that 30 days treatment with a probiotic mix activated the endocannabinoid system in zebrafish. These results highlight the potential of this probiotic mixture to regulate immune cell function, by inducing gene expression of toll-like receptors and other immune related molecules. Furthermore, TUNEL assay showed a decrease in the number of apoptotic cells, and this finding was supported by a reduction in pro-apoptotic factors and an increase in anti-apoptotic molecules. The results presented here strengthen the molecular mechanisms activated by probiotic mix controlling immune response and inflammation.