This study evaluated the effects of dietary supplementation of probiotic bacteria, Bacillus mycoides on the gut microbiota and health status of marron (Cherax cainii) under laboratory conditions. A total of 40 marron were randomly distributed into eight different tanks and two different groups in quadruplicates. The control group were fed only basal marron pellet while the second group were fed 108 CFU/g of probiotic bacteria in the diet. After 60 days of feeding trial, the health and immune indices of marron including protein and energy in the tail muscle, and total haemocyte counts in the haemolymph were positively influenced (p < 0.05) by the probiotic diet. The 16S rRNA sequence data revealed distinctly different microbial communities in the hindgut of marron with two different feeds after trial where Vibrio and Holdemania were the significantly abundant bacteria in the control and probiotic fed groups, respectively. In addition, the qRT-PCR analysis revealed upregulation of cytokine genes associated with the immunity and health status of crayfish indicated the beneficial effects of probiotic bacteria on the immune status of marron. Our results suggest that the diet supplemented with probiotic bacteria B. mycoides positively influenced the health status, immune indices and microbial composition of the marron gastrointestinal tract.