The biomass culture of biofloc for initially screening indigenous microbial strains recorded that most of the water quality parameters were within the appropriate growth thresholds for shrimp, the survival rate reached over 83% after 48 days of experiment. The method of bacteria isolation on selective media and molecular identification by sequencing the 16S rRNA gene segment discovered 04 isolates of metabolizing nitrogen, including 03 strains belonging to the species Nitratireductor kimnyeogensis (NQ1, NQ2, and NQ4 ), 01 strain highly similar to Hyphomonas polymorpha (NQ3), and 04 isolates relevant of creating biofloc were all the Bacillus genus (Bacillus sp. BQ1, B. velezensis BQ2, B. subtilis BQ3, and B. subtilis BQ4), with similarity from 98 to 100%. The highest transformation of ammonium and nitrate was strain NQ3, 96.1% and 83.7%, respectively. Strain NQ1 had the best nitrate removal efficiency (87.5%). Interestingly, the two strains BQ1 and BQ2 had good biofloc formation (78.3% and 55.8%), and simultaneously showed high proportions of ammonium metabolism (88.8% and 92.7%). Besides, the isolated strains could degrade organic substances and inhibit pathogenic bacteria. Particularly, strain BQ3 was able to decompose starch and cellulose, and strain BQ2 could decompose cellulose components and against Vibrio parahaemolyticus. As a result, 04 strains that met the criteria for application in shrimp farming using biofloc technology as NQ1, NQ3, BQ1 and BQ2 has been sellected.