Footrot is widely considered the most severe and most common foot pathology in small ruminants. This study tested the ability of a molecular typing system based on polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay of the 16S rRNA gene to discriminate between the strict anaerobe genera most commonly isolated from footrot ( Bacteroides, Dichelobacter, Fusobacterium, Porphyromonas and Prevotella ) in goats in Extremadura (Spain), with a view to facilitating identification for diagnostic purposes and thus providing a useful tool for future epidemiological studies. Although the electrophoretic patterns obtained with the enzyme Tru 1I were more readily interpreted, and may thus be the best initial option, results may be confirmed by a second enzyme ( RsaI). The PCR-RFLP assay of the 16S rRNA gene may therefore prove a useful addition to conventional biochemical identification techniques, providing taxonomic information at genus level.