Poly-phosphate accumulating bacteria (PAB) is an important bacterial group that can take up large amounts of phosphate and accumulate as intracellular poly-phosphate, contributing to biological phosphorus removal in waste-water treatment. The study was conducted to analyze a genetic diversity of PAB community isolated from samples of water and sludge of intensive catfish ponds and effluent water and sludge obtained from piggery waste-water treated by bio-digesters in the Mekong Delta, Vietnam. In a total of 439 isolates, there are 48 isolates that have the potential of accumulating intracellular poly-phosphate shown main characters included shaped like a rods or short rod-shaped; motile, twitching movements or non-motile; expression of poly-phosphate electron dense granules within the cells; accumulated poly-phosphate from poly-phosphate kinase gene 1; the content of intracellular poly-phosphate varied from 10-9 to 10-12 mg/cell. Based on phylogenetic tree for partial 16S rRNA genes, there are 22 strains isolated from intensive catfish ponds included in four classes: Bacilli, Actinobacteria, Beta-proteobacteria, Gamma-proteobacteria, and 26 strains isolated from piggery waste-water treated by bio-digesters included in four classes: Bacilli, Actinobacteria, Alpha-proteobacteria, Gamma-proteobacteria. The process of analysis and comparison of genetic diversity of 48 isolates showed 16S rRNA sequences have nucleotide regions of high variability interspersed with nucleotide regions of low variability. The variation of o and Pi index formed the different types of haplotype in population of PAB, there were 25 haplotypes (genotypes) from 48 sequences. The difference of the structure of haplotypes formed a high diversity between them (Hd=0.91). The levels of haplotype diversity created many genotypes for the genetic variation and the ability to adapt to the environment in the evolutionary process of bacterial strains capable ofhigh accumulating poly-P. Comparison of genetic diversity between populations of bacteria isolated from two sampling places, the results showed that the nucleotide and haplotype diversity of the strains isolated in piggery waste-water treated biodigesters (Pi=0.16, h=14) were lower and the genetic conservation was higher than isolated strains in intensive catfish ponds (Pi=0.18, h=16). This is scientific basis for the selection of the sample sources for the isolation and selection of poly-phosphate accumulating strains.