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Chromoblastomycosis is a chronic severely mutilating disease caused by fungi of the order <i>Chaetothyriales</i>. Classically, <i>Phialophora verrucosa</i> has been listed among these etiologic agents. This species is known to occur in the environment and has been found to cause other infections like phaeohyphomycosis, while reported cases of chromoblastomycosis are scant. <i>Phialophora</i> is phylogenetically diverse, and thus retrospective confirmation of etiology is necessary. We studied ten proven cases of chromoblastomycosis from Mexico and further analyzed the population genetics and genomics of the <i>Phialophora</i> species to understand their pathogenicity and predilection. The clinical strains were molecularly identified as <i>Phialophora americana</i> (<i>n</i> = 4), <i>Phialophora</i><i>chinensis</i> (<i>n</i> = 4), and <i>Phialophora macrospora</i> (<i>n</i> = 2). No genetic distinction between clinical and environmental strains was possible. Further analysis of strains from diverse origins are needed to address eventual differences in virulence and niche predilection between the species.