Burkholderia cepacia was originally described as the causal agent of onion sour skin. However, this bacterium is now recognized as a complex of 22 closely related species, commonly referred to as the B. cepacia complex (BCC). Only a few taxonomic studies have been undertaken with the aim of understanding the diversity of species associated with onion sour skin. In this study, we used a polyphasic analysis including rep-PCR assay, biochemical and pathological profiles, and multilocus sequence analysis (MLSA) to characterize the BCC species associated with onion sour skin in the semi-arid region of north-east Brazil. Phylogenetic analysis of the recA of strains representing the genetic variability, as determined by rep-PCR, grouped the strains into four clades. Clades I and II represent B. cenocepacia lineages IIB and IIIA, respectively, while the strains in Clades III and IV clustered more closely to Clades I and II than to strains of any other BCC species. MLSA confirmed the existence of the four clades with a 1.00 posterior probability. A distance matrix indicated a low level of divergence among the strains of the four clades found in the MLSA, proving that B. cenocepacia lineages IIIA, IIIB, and a new lineage of B. cenocepacia are associated with onion sour skin in the semi-arid region of north-east Brazil. Also, surprisingly, no strain was identified as B. cepacia, indicating that this species probably does not play a role in this disease in this region.