Chronic tropical cutaneous ulcers remain a neglected medical condition in West Africa, particularly Buruli ulcer, which is caused by mycolactone cytotoxin-secreting Mycobacterium ulcerans ( M . ulcerans ). Medical management of this highly debilitating and necrotising skin infection may be modified by colonisation and co-infection of the ulcer by opportunistic and pathogenic microorganisms, which considerably delays and increases the cost of treatment. Methodology/principal finding We diagnosed chronic tropical cutaneous ulcers in nine patients in Côte d’Ivoire using M . ulcerans -specific PCRs and culturomics. This revealed M . ulcerans in 7/9 ulcer swabs and 5/9 control swabs as well as an additional 122 bacterial species, 32 of which were specific to ulcers, 61 specifics to the controls, and 29 which were shared, adding 40 bacterial species to those previously reported. Whole genome sequencing of four Bordetella trematum ( B . trematum ) isolates in four Buruli ulcer swabs and no controls indicated cytolethal distending toxins, as confirmed by cytotoxic assay. Conclusions/significance In four cases of Buruli ulcer in Côte d’Ivoire, B . trematum was a co-pathogen which was resistant to rifampicin and clarithromycin, unmatching M . ulcerans antibiotic susceptibility profile and counteracting the current treatment of Buruli ulcer in West Africa and Australia. Thus, we report here chronic mixed M . ulcerans - B . trematum chronic tropical ulcer as a specific form of Buruli ulcer in West Africa.