Indigenous microorganism (IMO) has great potential in agricultural uses since they have high ability in biodegradation, nitrogen fixation, phosphate solubilization, plant growth hormone production as well as bio-control. However, deeply scientific knowledge about IMO has been limited and should be elucidated. The aim of this study was to isolate bacteria having both functions in biological nitrogen fixation and indole-3- acetic acid synthesis from IMO in different farming ecosystems in Soc Trang province, Vietnam. Nitrogen fixing bacteria were isolated on free N element Burk agar medium. NH4 + concentration in Burk liquid medium was determined by nitroprusside reagent method at a wavelength of 650 nm for total nitrogen and 636 nm for available ammonium. In addition, nifH functional gene involving in nitrogen fixation was also detected by specific polF/polR primers for some best isolates. The IAA synthesizing capacity of bacteria was assessed quantitatively by Salkowski's reagent method at a wavelength of 530 nm. The results showed that from 19 different indigenous microbial communities 83 isolates in total able to fix nitrogen were obtained. Quantitative tests showed that bacteria fixed total nitrogen and IAA synthesis varied between 0.58 and 22.55 µg.mL-1 and between 0.85 and 58.04 µg.mL-1. Among them seven isolates labeled as TP-1.3, TP-1.4, MQ-2.1, MQ-2.5, MT16.5, OM-17.2 and OM-17.5 were identified as highest nitrogen fixers having also other function of IAA synthesis with amount of 0.86, 4.23, 1.37, 0,42, 1.15, 1.76 and 1.83 µg.mL-1, respectively for available ammonium and 27.54, 26.98, 23.99, 35.32, 58.04, 41.87 and 29.44 µg.mL-1respectively for IAA. Particularly, all twenty-two tested bacteria showed a present of functional nifH gene for biological nitrogen fixation in their genetic structure. Results of 16S rARN ribosomes sequences of seven best bacteria indicated that TP-1.3 had 99% identification index with Paraburkholderia tropica, TP-1.4 and MQ-2.1 had highly similarity (99%) with the strain of Paenibacillus cineris and Bacillus aryabhattai while MQ2.5 and OM-17.5 were highly homologous with Bacillus megaterium and MT-16.5 and OM-17.2 had a highly homologous sequence as Klebsiella pneumoniae. These nitrogen fixing bacteria have other function in IAA synthesis can be used for sustainable agricultural cultivation in Soc Trang province.