Sixty-eight entophytic bacterial isolates were isolated from 70 soybean nodules of soybean plants which collected at Buonho town, DakLak province (38), Cujut district, DakNong province (19) and Can Tho city, Mekong Delta (11), Vietnam; they developed on two kinds of medium (PDA and TSA) after 2 or 3 days incubation and they made the pellicles on semi-solid media. The bacterial isolates were tested in-vitro for plant growth promoting properties including nitrogen fixation, phosphate solubilization and IAA production together with evaluating effects on the growth of soybean plants on pots. All of them had the ability of ammonium synthesis, phosphate solubilization and IAA biosynthesis however the isolates originated from western highland (DakLak and DakNong province(s)) having the big potential of phosphate solubilization in comparison to the isolates from Can Tho city (Mekong Delta). The sequences from selected nitrogen-fixing and phosphate-solubilizing bacteria (16 isolates) showed high degrees of similarity to those of the GenBank references strains (between 97% and 99%). From 16 isolates, 9 belonged to Bacilli and 7 were Gamma-Proteobacteria. Based on Pi value (nucleotide diversity), Bacilli group had highest Theta value and Thete values (per sequence) from S of SNP for DNA polymorphism were calculated from each group and Bacilli group had the highest values in comparison to gammaproteobacteria. From these results showed that there are two strains as Paenibacillus lautus CJE17 and Bacillus megaterium CJE10 revealed promising candidates with multiple beneficial characteristics and they have the potential for application as inoculants adapted to poor soils and local crops because they are not only best strains but also combine with rhizobia strains for improvement of good grain yield and quality seed of soybean cultivation on ferralsols in the future.