The endemicity of Buruli ulcer (BU), a non-tuberculous mycobacteria infection, has significantly increased in Côte d'Ivoire. The exact transmission mode remains unknown but DNA based evidence of Mycobacterium ulcerans, the causative agent, have implicated potential environmental reservoirs, similar to those suspected in the transmission to humans. The role of small mammals in transmission has recently received some research attention. Based on the hypothesis that the overlapping ecology of human and animal habitats would favour mycobacteria transmission, the study aimed to identify BU like infections in small mammals living in close proximity to humans, in endemic communities. One hundred and eleven animals were trapped within five communities in two major endemic areas, Daloa and Tabbo. Majority of trapped small mammals were mice, Mastomys natalensis, of which 8 animals had external lesions. PCR on organ and lesion samples identified, predominantly, mycobacterium spp, of which five mice were positive for IS2404. IS2404 sequencing confirmed infection in two mice as M. ulcerans strain Agy99.