Antimicrobial resistance in the food chain is currently a subject of a major interest. The excessive use or rather misuse of antimicrobials coupled with a poor hygiene in the food production chain has led to a rise of resistant zoonotic bacteria, commonly transmitted by food. They pose a serious threat to human health. Campylobacteriosis is the leading bacterial food-borne illness and most commonly reported zoonosis in humans in the European Union for more than a decade. Salmonellosis is most frequently diagnosed in food-borne outbreaks. Fluoroquinolones are considered as critically important for treatment of severe cases of both zoonoses in humans. Due to an extremely prevalent resistant isolates, especially from broilers and meat, also the treatment of human Campylobacter infections with fluoroquinolones has become compromised. Salmonella isolates from poultry and poultry meat tend to be highly resistant to fluoroquinolones as well. Beside the resistance to this group of antibiotics, the threat of multiple drug resistant (MDR) Campylobacter and Salmonella strains is discussed in the light of most recent reports of animal, food and human clinical surveillance systems.