ABSTRACT. Equine canker is a chronic pododermatitis of the hoof in horses. Although spirochetes are detectable histopathologically in the lesions, the precise etiology remains unclear. This study reports the 16S rRNA gene sequencing of randomly selected clones based on PCR with Treponema-specific primers, using the canker lesions from two horses and healthy frog and sole from a horse. A total of 114 clones were obtained from the lesions, but no clones were detected in the healthy hoof tissues. The clones from the canker lesions examined were grouped into 19 operational taxonomic units, such as treponemal phylotypes originating from papillomatous digital dermatitis lesions of dairy cattle and as-yet uncultured human oral treponemes, indicating the presence of multiple treponemes in the lesions. Equine canker is a proliferative pododermatitis of horses manifested as chronic, hyperproliferative, suppurative, or pyogranulomatous dermatitis in the frog, bars, and sole, and (in severe cases) the adjacent hoof wall [11]. Grossly, the lesion appears as a soft, whitish, cauliflower-like proliferation associated with a foul-smelling caseous exudate. Histopathologically, the excised tissues show a markedly hyperplastic and hyperkeratotic epithelium with radiating bands of neutrophilic inflammation.Recently, spirochetes were detected histopathologically in canker lesions of Tennessee walking horses using the modified Steiner staining technique, and this demonstrated numerous spirochetes extending into the proliferative epithelium [9]. The authors [9] suggested that spirochetes may contribute to the pathology of equine chronic foot diseases, in a similar manner to the way in which spirochetes contribute to that of bovine papillomatous digital dermatitis (PDD) and contagious ovine digital dermatitis (CODD). Although the spirochetes detected in PDD and CODD have been identified as the genus Treponema [4,5,7,12,14,16,17], the phylogenetic relationship of the spirochetes detected in canker lesions remains unclear.To determine the spirochete phylogeny, we used 16S rRNA gene sequencing of randomly selected clones based on PCR with Treponema-specific primers to search for treponemes present in canker lesions in this study. Furthermore, we searched for the presence of treponemes in healthy hoof tissues. To our knowledge, this is the first reported molecular investigation of spirochetes from equine canker lesions.