The aim of this study is to determine the bacterial flora of intestine in sturgeon juvenile in earthen ponds which the results can be applied to prevent diseases and hygiene management of sturgeon during rearing in earthen ponds which leads to commercial benefits and sturgeon stock rehabilitation. Stability of bacterial flora in fish intestine is very significant, because the intestine is an important place for out break of microbial infections and other fish diseases. This is specially notable when the fishes have not Vaccinated. In this study, random sampling conducted and 90 Persian sturgeon (Acipenser persicus) having 3-5g weight, collected by trawling in 3 earthen ponds. ofter recording of biometrical characteristics the intestine and rearing water, were cultured on TSA medium. After 24-48 h, the total bacteria counted based on CFU (colony-forming unit) in 20oC. gram staining and complementary experiments conducted. Also, physicochemical factors of ponds determined. In order to identify the bacterial species, various biochemical experiments carried out using the tests described by Holt et al. (1994).The results showed that the mean temperature is 25.6±0.5oC, oxygen 4.6±1.48 (mg/l), pH= 8.05±0.5, NO2=0.06±0.01 (mg/l), NH4=0.24±0.08 (mg/l), PO4= 0.17 (mg/l). According to biometrical recording, in this study, the mean weight and length of juveniles were 5.59±3.18 and 11.4±2.9, respectively.The results showed that the mean facultative aerobic and anaerobic bacterial counts in intestine were 5.59±0.92 (log CFU/g) and 6.67±0.34 (log CFU/ml) in Acipenser persicus juveniles and rearing water, respectively. Furthermore, the following bacteria determined in intestine of Persian sturgeon: Aeromonas sp, Aeromonas sorbia, Aeromonas hydrophyla, Entrobacteriaceae, Corynebacteriun. The dominant bacterium in intestine was Aeromonas sp. The bacteria in the rearing water were Aeromonas sp and Aeromonas soberia which Aeromonas sp was the dominant one.