Relatively poorly developed digestive and immune systems appear as key factors for low survivability and reduced growth rate of major carp during early development stages. Here, an attempt has been made to improve the digestive capability and immune response of Labeo rohita larvae by feeding diets supplemented with yeast and bacterial based probiotics Geotrichum candidumQAUGC‐01 and Bacillus cereus,locally isolated from yogurt and gastrointestinal tract of an adult healthy L. rohita respectively, and evaluate their effects on the survival, growth, digestive enzyme activity, muscle composition and intestinal bacterial load. Eleven week feeding experiment in triplicate with four groups was conducted in a completely randomized design. Control group was given only basal feed devoid of probiotic, T1 and T2 groups was provided basal diet supplemented with G. candidum and B. cereus respectively at similar rate, that is, 1 × 109 CFU/g feed, while T3 group was fed a diet supplemented with consortium of both probiotics, each at the rate of 1 × 109 CFU/g feed. G. candidum showed the most significant effect (p < 0.001) on final weight, SGR, biomass, survival (%), microbial gut count and muscle composition. Intestinal enzymes activities also showed significant variation, as amylase activity was significantly (p < 0.001) higher in T1, while T3 group of fish showed higher activity of cellulase and protease. Likewise, after challenge with Aeromonas hydrophila, T1 group showed significantly (p < 0.001) higher survival. This study signifies the higher efficiency of G. candidum in comparison to B. cereus and suggests its inclusion in the diet for early rearing of L. rohita.