Campylobacter concisus is a fastidious, hydrogen-requiring, gram-negative bacterium found in the human oral cavity. It is an opportunistic pathogen as it has been isolated from periodontitis, gastroenteritis, and more recently from intestinal biopsies of Crohn’s disease patients. C. concisus strains have been grouped into two genomospecies (A&B) according to the PCR amplification of the 23s rDNA. They were also allocated into 4 genomic clusters based on the amplified fragment length polymorphism analysis technique (AFLP). The diversity of C. concisus strains was also confirmed after sequencing the genome of two C. concisus strains (C. concisus13826 and UNSWCD) revealing that the number of genes was not similar in their genomes. In this study, the presence of some putative virulence genes in the genome of thirty-four C. concisus isolates from oral and clinical origins, assigned to two genomospecies, was investigated by PCR amplification. Oligonucleotides were designed based on the genome sequence of C. concisus13826 for the detection of the cjaC gene encoding for antigen C; the dnaj gene encoding for a heat-shock protein; the flaB gene encoding for Flagellin B and the flaC gene encoding for the Flagellin-like protein FlaC. Other Campylobacter species including C. mucosalis, C. jejuni and C. coli were also tested. Our findings suggest that PCR products for the cjaC, dnaJ, and flaB genes can only be amplified in C. concisus strains belonging to genomospecies B, indicating that genomospecies A strains might have variations in their genome sequences compared to C. concisus13826 genome. However, the PCR amplification of the flaC gene was achieved for all C. concisus tested strains. These results emphasize the heterogeneity of this organism according to its genomic level. Findings from our research will significantly add to the current volume of knowledge and thereby aid in a better understanding towards C. concisus genetic diversity. Further studies are required to evaluate the virulence of these isolates.