The aim of this study was to assess the effects of nucleotide on intestinal microbiota of striped catfish, Pangasianodon hypophthalmus. Different levels of the NT (0, 0. 25. 0. 5, 0. 75 and 1 % weight per weight, WW-1) were added to basal diet and then randomly allocated to triplicate groups of fish with average initial weight (1. 52± 0. 11 g) for 10 weeks. At the end of the experiment, at least 10 individual fish from each treatment were used to study quantitative and qualitative analyses of bacterial flora of intestine. The bacterial flora was identified to species level where possible. Total viable bacterial counts in the intestine of the catfish ranged from 4. 33± 0. 49×104, 5. 98± 0. 82×104, 6. 44± 1. 09×104, 5. 54± 0. 64×104 and 2. 65± 0. 46×104 colony forming units (cfu/g) for groups treated with 0-1% NT respectively without any significant difference among groups (P>0. 05). Gram negative rod shaped bacteria were dominant in all groups. Altogether 16 bacterial species of 12 genera were identified in total populations. Most of the bacterial species were common among all groups. Proteus mirabilis, Serratia liquefaciens, Bacillus cereus only were observed in NT treated fish while Alkaligenes faecalis only existed in the control group. Corynebacterium urealyticum and Staphylococcus aureus were identified in some fish belong to control-0. 25 NT and control 1-NT groups respectively. The results of this study demonstrate that although the total bacterial count number did not affected by dietary NT but some qualitative changes were clearly observed.