The effect of dietary administration of probiotic Lactococcus lactis MM1 for 60 d on the autochthonous microbiota in the foregut, midgut and hindgut of juvenile grouper, Epinephelus coioides, was evaluated using polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE). Samples collected from the probiotic and control groups showed different DGGE patterns, while 11 common bands presented in both groups. The similarity dendrogram revealed three different clusters depending on the three sections of the gastrointestinal (GI) tract, and the probiotic triplicates in each GI section were generally clustered into one group distinctly different from the corresponding control triplicates. Increased species richness and Shannon index were observed in the foregut, midgut, and hindgut samples in the probiotic group compared with the control group, which suggested that probiotic L. lactis MM1 could improve the autochthonous microbial diversity along the GI tract of E. coioides. The growth of many potentially beneficial and unidentified bacteria was stimulated by the probiotic, whereas the growth of some potential harmful species, like Staphylococcus saprophyticus, was depressed.