Banana (Musa spp.) is one of the most widely cultivated subtropical fruits around the globe. Banana cultivation has been extensively increased in southeastern Iran over the last two decades. Recently, banana fruits possessing rotten and blackened fingertip symptoms were observed in Sistan‐Baluchestan, Iran. Isolation and characterization of the causal agent showed that the pathogen belongs to the multifaceted bacterial species Burkholderia cenocepacia. Pathogenicity tests and host range assays showed that the strains were pathogenic on banana, as well as carrot, onion and potato. All the strains were resistant to 50 mg L−1 rifampicin and 200 mg L−1 copper sulphate. Phylogenetic analysis of 16S rRNA and recA gene sequences showed that the strains belong to two different genomovars of B. cenocepacia (III‐A and III‐B), which also include environmental and cystic fibrosis associated strains of the species. The results obtained from recA phylogeny were confirmed using multilocus sequence analysis (MLSA), although MLSA showed that the banana strains were clustered as a novel phylogroup among the members of both genomovars. Banana‐pathogenic B. cenocepacia strains isolated in Iran were different from the strains isolated in Taiwan, as the ‘B. cepacia epidemic strain marker’ reported in the Taiwanese strains was absent from Iranian strains. To the authors’ knowledge, this is the first MLSA‐based study on the banana‐pathogenic strains of B. cenocepacia. However, further in‐depth molecular studies are needed to decipher the relationships between the banana fingertip rot pathogen and the clinical strains of B. cenocepacia.