Three hundred and one (301) isolates were isolated onto the Minimal medium, 202/301 isolates (67.11%) were identified with universal primers (Pseudomonas sp.) and 185/202 isolates (91.58%) were determined with the specific primers (Pseudomonas stutzeri). Therefore, the identification of Ps. stutzeri with 2 pairs of primers ensured certainly. Many strains had the good ability of ammonium oxidation (amo genes), many strains had the good ability in oxidized nitrite and nitrate, they has been applied in wastewater treatment as water in TRA-fish ponds infecting ammonium and piggery wastewater. Besides, many Pseudomonas stutzeri strains were discovered the presence of nif genes and they were used as biofertilizer for rice cultivation, some Pseudomonas stutzeri strains had phyt gene in their genome and they were used as source of supplementary for pigs, chickens and TRA-fish feeds. The diversity of Pseudomonas stutzeri in soils and water in the Mekong Delta, Vietnam is plentiful and their applications were applied in many aspects as wastewater treatment, biofortilizers production and supplemaentary feeds.