Campylobacter concisus is recognized as a potential pathogen in gastrointestinal diseases, particularly in patients with chronic intestinal diseases. This study investigates the genomic characteristics, phylogenetic distribution, virulence factors, resistance genes and presence of plasmids in C. concisus isolates from Slovenian patients with community-acquired infectious diarrhoea. Prospectively collected isolates were analysed using whole-genome sequencing (WGS). WGS analysis revealed substantial genetic diversity among isolates, with distinct differences observed between two genomospecies (GS1, GS2). GS1 isolates had smaller genomes, lower GC content, and fewer coding regions than GS2 isolates. Multilocus sequence typing confirmed a high degree of genetic diversity, with most isolates belonging to novel sequence types. Plasmids, including pSma1 and pICON, were more prevalent in GS2 isolates. The virulence factors Zot and Exo9 toxins were detected in both genomospecies, with Zot predominantly found in GS1 and Exo9 in GS2. The T6 secretion system was prevalent in both groups, whereas the T4SS was less frequently observed. The combination of the T6SS, plasmids, and toxins suggests a complex mechanism of pathogenicity. This study highlights the high genetic diversity of C. concisus and provides new insights into its genomic features and virulence factors. The presence of plasmids and secretion systems, particularly the T6SS, underscores the potential of C. concisus for adaptation and pathogenicity.