Currently only phenotypic epidemiological markers, serogrouping and virulence testing of Dichelobacter nodosus, are available for investigating footrot outbreaks in small ruminants. These methods have limitations in tracing the source of infection. In this study, a genotypic marker, PCR–RFLP of outer membrane protein gene, was used to characterize D. nodosus. The technique was evaluated in a controlled experiment involving two strains of bacteria. PCR–RFLP was found to be highly specific in differentiating isolates obtained from recipient animals infected with different strains. Subsequently, this technique was used to characterize isolates obtained from field cases of footrot in Nepal. A total of 11 patterns was recognized among 66 Nepalese D. nodosus isolates representing four different serogroups. PCR–RFLP also discriminated isolates with similar phenotypic characteristics. However, all isolates which, phenotypically, were virulent were represented by only two patterns irrespective of their serogroups. It is suggested that PCR–RFLP described here could be a useful epidemiological marker in the study of footrot.