Probiotic is considered as a remedy to solve disease problem in shrimp aquaculture. Shrimp body and environment bacterial flora are recommended as reliable source for extracting of beneficial bacteria. Therefore, 5000 pieces of post larvae of Penaeus monodon were distributed equally in 4 tanks in probiotic and antibiotic free condition up to juvenile. Then microbiological samples from digestive system, muscles, body surface, rearing water and tank sediment were inoculated onto the selective media plates. Incident of total bacteria, Vibrio, Pseudomonas and Entrobacteriaceae were evaluated in different body parts and rearing environment of shrimp. The highest bacteria count for total bacteria, Vibrio, Pseudomonas was occurred in sediment followed by digestive system. No Entrobacteriaceae was observed from all samples. Isolated bacteria were identified and placed in 7 genera consisted of Vibrio, Shewanella, Burkholderia, Clavibacter, Staphylococcus, Brevibacterium, Corynebacterium, while one genus remained unidentified. Genus Shewanella exhibited highest frequent bacteria in digestive system of P. monodon which may be indicated its ability to colonization in digestive system. Shewanella algae was selected from whole isolated bacteria as candidate probiotic via well plate diffusion technique and cross streak antagonistic test against Vibrio harveyi, V. parahaemolyticus and V. alginolyticus. It was able to digest lipid and protein in tributyrin agar and skim milk agar.