Burkholderia is an important bacterial genus containing several species of ecological, biotechnological and pathological interest. Bacterial isolate can be gotten from soil, water, plants and even clinics. With their taxonomy undergoing constant revision and the phenotypic similarity of several species, correct identification of Burkholderia is difficult. Burkholderia cepacia complex (Bcc) consists of nine discrete genomic species and a genetic scheme based on the recA gene has greatly enhanced the identification of B. cepacia complex species. The objectives of this study were to identify Burkholderia strain UPM B3 which was isolated from oil palm roots to the species level based on Biolog Identification System, and to carry out DNA fingerprinting for strain differentiation as well as differentiate between pathogenic and non-pathogenic human forms. Antagonistic activity of UPM B3 against Ganoderma boninense was also evaluated by using dual culture and poison food tests. Genotype characterization was carried out by amplification of the recA gene using specific primers, purified using QIA Quick polymerase chain reaction (PCR) purification kit and sequenced. Multiple sequence alignments were performed on closely related sequence accessions using CLUSTAL W software. Result of nucleotide sequencing followed by phylogenetic analysis of the recA fragments differentiated both putative and known Burkholderia species and all members of the B. cepacia complex. Genomovar analysis confirmed that UPM B3, isolated from oil palm roots belongs to genomovar I and has antagonistic activity against G. boninense based on in vitro dual culture and poison food tests. From the phylogenetic tree, UPM B3 is a specific strain within B. cepacia complex species that belong to genovomar I which is associated with strains nonpathogenic to humans. Thus, B. cepacia strain UPM B3 has the potential to be used against G. boninense, the causal pathogen of basal stem rot (BSR) in oil palm.