With a rising demand for shrimps in the world, the industry turns to aquaculture as a substitute to wild catch shrimps to meet the consumer’s demand. However, it becomes effortless for diseases such as Acute Hepatopancreas Necrosis Disease (AHPND) caused by Vibrio parahaemolyticus to spread due to high density cultures causing high mortalities and economic losses. The aim of this study is to evaluate the growth performance, gut microbiota and resistance to challenge with V. parahaemolyticus of Peanneus vannamei. The shrimps were fed at 5% body weight with 1.0, 2.0 and 3.0% of Sargassum polycystum supplemented diet. Shrimps (0.015 ± 0.001) in triplicate groups with a density of 30 shrimps per tank were fed the diets twice daily for 6 weeks and results were compared to shrimps fed with a control diet without any supplementations. At the end of the feeding trial, shrimps fed with S. polycystum supplemented diet has significantly higher growth of gut microbiota and a higher rate of survival compared to the control group (P < 0.05). However, there was no remarkable difference in growth and resistance challenge with Vibrio parahaemolyticus (P > 0.05). Overall, the use of S. polycystum was not useful in the improvement of growth of the shrimps however, it is effective as a prebiotic to increase the growth of gut microbiota which could lead to the reduced use of antibiotics in the shrimp industry.