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¹ Sri Venkateswara Veterinary University, College of Fishery Science, Department of Aquatic Animal Health Management, Muthukur- 524 344 Nellore, Andhra Pradesh, India DOI : 10.4194/TRJFAS20130 Viewed : 1831 - Downloaded : 1764 The microbial composition of rearing water, growth and immune status of Litopenaeus vannamei juveniles in biofloc (T1), substrate-integrated biofloc (T2), substrate (T3) systems and a control with four replicates each were evaluated in a 49-day indoor trail. In each HDPE tank of 70 L capacity filled with 10 g L-1 salinity water, ten shrimp (4.56±0.13 g) were stocked. The C: N ratio of 15:1 was maintained in T1 and T2 using wheat flour as carbon source for production of biofloc. The TAN, NO2 and NO3 were lower (P<0.05) in treatment tanks than that in control. It was also observed that the counts of Bacillus, Lactobacillus, Vibrio and zooplankton were high in T2 than T1, T3 and control. There was higher net weight gain (10.38±0.14 g) and lowest FCR (1.27±0.12) with T2 when compared to T1, T3 and control tanks. Moreover, the survival rate is significantly higher in treatments than control. Significant increase in THC (47.24±4.49 x 106 cells ml-1), serum protein (82.67±0.01 mg/ml), Phenoloxidase (0.73±0.03, OD 490 nm) and Lysozyme activity (56.32±0.03%) was observed in T2 than T1, T3 and control. The result shows that substrate-integrated biofloc system assures higher growth, survival and better immune response in L. vannamei. Keywords : Biofloc, Substrate, L. vannamei, Water quality, Immune response