Abstract: The study was undertaken with the aims of identifying Prevotella intermedia virulent strains from adult periodontitis and to detemine its virulent gene via molecular analysis. The clinical isolates were assessed for their potential and ability to produce toxin and form skin lesion in balb/c mice. Infected mice appeared cachectic and the histological effect of the skin lesion showed that all lesions were localized at the injection site and causes tissue damage with skin necrosis and hair loss. Prevotella intermedia UMD 5 was the most virulent isolate and thus was selected for shotgun cloning. Partially digested genomic DNA (2-9 kb) from P. intermedia UMD 5 was cloned into the Bam HI site of E. coli pUC 18. The inserted gene for all recombinant clones was expressed in balb/c mice. It was found that only one clone was able to induce localized skin lesion in mice. The cloned gene expressed well by inducing skin lesion in mice when incubated in aerobic environment, but the expression was better in combination of aerobic followed with anaerobic environment, producing bigger skin lesion area in balb/c mice. Thus, the presence or absence of O₂ did not suppress the level of toxin production for anaerobic bacterial gene cloned in the aerobic system. Histological effect of the skin lesion showed that lesions were localized at the injection site and causes tissue damage with skin necrosis and hair loss. In addition, the recombinant plasmid was found to be stable in the host system. The clone was further analyzed via restriction analysis and was found to have a DNA insert of 4 kb.