Immunosuppression is a manifestation imbalance in the immune system, often during unhealthy states. In recent years, lactic acid bacteria (LAB) have been found to be important components of the body's innate immune system, and indispensable to maintaining normal immune function. Lactobacillus plantarum BF_15, a novel strain isolated from the feces of breast-fed infants, which has shown potential as an immunomodulator in vitro. In the present study, with the Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) based on RNA-polymerase beta subunit encoding gene (rpoB) to analyze the colonization of L. plantarum BF_15 in the intestine of mice. In addition, Lactobacillus rhamnosus GG (LGG) as a positive control strain, by measuring immune-related indexes and the diversity of intestinal microbiota, the effects of BF_15 on immunoregulation and intestinal microbiota dysbiosis were investigated to elucidate whether the attenuation of immunosuppression is related to the modulation of intestinal microbiota. Results did indeed support this notion that BF_15 did colonize murine intestines well, in which it could still be detected in mice feces 14 days after stopping the probiotic administration. Moreover, BF_15 found to protect mice against reduction in the levels of several immune-related indicators, including the thymus and spleen indexes, splenic lymphocyte proliferation, toe swelling degree, serum hemolysin-antibody level, and macrophage phagocytosis index, triggered by high-dose (200 mg kg-1) intraperitoneal administration of cyclophosphamide (CTX). In addition, the strain was also found to effectively balance intestinal microbiota dysbiosis in the mice. Collectively, these results indicated that L. plantarum BF_15 can not only successfully colonize murine intestines, but also can effectively alleviate CTX-induced immunosuppression, once established, by rebalancing the intestinal microbiota. This, therefore, provides strong evidence for the view that BF_15 has the potential to become a highly effective immunomodulating probiotic in human microbiota as well.