<jats:p><jats:italic>Campylobacter</jats:italic>spp., especially<jats:italic>C. jejuni</jats:italic>, are recognized worldwide as the bacterial species that most commonly cause food-related diarrhea.<jats:italic>C. jejuni</jats:italic>possesses many different virulence factors, has the ability to survive in different reservoirs, and has shown among isolates the emergence of Antimicrobial Resistance (AMR). Genome association analyses of this bacterial pathogen have contributed to a better understanding of its pathogenic and AMR associated determinants. However, the epidemiological information of these bacteria in Latin American countries is scarce and no genomic information is available in public databases from isolates in these countries. Considering this, the present study is aimed to describe the genomic traits from representative<jats:italic>Campylobacter</jats:italic>spp. strains recovered from faecal samples of patients with acute diarrhoea from Valparaíso, Chile.<jats:italic>Campylobacter</jats:italic>spp. was detected from the faeces of 28 (8%) out of 350 patients with acute diarrhoea, mainly from young adults and children, and 26 (93%) of the isolates corresponded to<jats:italic>C. jejuni</jats:italic>. 63% of the isolates were resistant to ciprofloxacin, 25.9% to tetracycline, and 3.5% to erythromycin. Three isolates were selected for WGS on the basis of their<jats:italic>flaA</jats:italic>-RFLP genotype. They belonged to the multilocus sequence typing (MLST) clonal clomplex (CC) 21(PUCV-1), CC-48 (PUCV-3), and CC-353 (PUCV-2) and presented several putative virulence genes, including the Type IV and Type VI Secretion Systems, as well as AMR-associated genes in agreement with their susceptibility pattern. On the basis of the wgMLST, they were linked to strains from poultry and ruminants. These are the first genomes of Chilean<jats:italic>C. jejuni</jats:italic>isolates available in public databases and they provide relevant information about the<jats:italic>C. jejuni</jats:italic>isolates associated with human infection in this country.</jats:p>
