Burkholderia cepacia complex (BCC) is a group with high genetic versatility and adaptability. It contains at least 90 valid species belonging to the subphylum of β-proteobacteria, gram-negative bacilli ubiquitous bacteria in a wide range of niches. We isolated three Burkholderia species with different interactions with the rice plant as the host plant. Burkholderia vietnamiensis strain J14Eple2 (accession number: SAMN24971778) has plant growth-promoting properties and antimicrobial activities against Rhizoctonia solani AG1IA, the causal agent of rice sheath blight. While B. cepacia strain J14Eple (accession number: SAMN24971777) and B. gladioli strain A12Epstem have pathogenicity properties, and they can induce a Hypersensitive response in tobacco leaves. The complete genome of B. vietnamiensis strain J14Eple2 and two pathogenic Burkholderia species, including B. cepacia strain J14Eple and B. gladioli strain A12Epstem isolated from rice, was sequenced, analyzed, and annotated to find B. vietnamiensis strain J14Eple2 potential virulence, the gene regions related to virulence, antibiotic resistance and antibiotic production, were compared between non-pathogenic B. vietnamiensis strain J14Eple2 and two pathogenic Burkholderia species, including B. cepacia strain J14Eple and B. gladioli strain A12Epstem. The genomic analyses reveal that non-pathogenic B. vietnamiensis strain J14Eple2 habor genes are encoding occidiofungin that has excellent potential for developing biopesticides and pharmaceutical drugs while not detected in pathogenic Burkholderia species. In the Non-pathogenic B. vietnamiensis strain J14Eple2, 12 Genomic Islands were identified, while the pathogenic B. cepacia strain J14Eple and B. gladioli strain was found A12Epstem 14 and 19 GIs identified. For examining the ability of B. vietnamiensis strain J14Eple2 in pathogenicity in mammalian and opportunistic infections in cystic fibrosis patients, we searched in the genome of B. vietnamiensis strain J14Eple2 to find essential virulence factors such as Cable pili, 22-kilodalton adhesion biosynthesis genes, SodC gene, zink metalloprotease, melanin pigment, VgrG-5 protein. We found B. vietnamiensis strain J14Eple2 does not harbor genes of essential virulence factors such as encoding Cable pili and VgrG-5 protein. Nevertheless, it has some genes encoding CF-related O-antigen biosynthesis. Our result suggests that regardless of strong antimicrobial activity and plant growth-promoting features of B. vietnamiensis strain J14Eple2, It is better to avoid direct use in Agriculture. However, B. vietnamiensis strain J14Eple2 has Quorum quenching potential and can be used to produce QQ molecules.