The potential of a fingerprinting method based on the single-enzyme amplified fragment length polymorphism (s-AFLP) technique was evaluated for its efficacy in detecting foodborne Campylobacter and Arcobacter species. Campylobacter and Arcobacter isolates from chicken and water samples were subjected to s-AFLP and pulsed-field gel electrophoresis (PFGE) profiling. Molecular typing revealed a high degree of heterogeneity. AFLP was found to be appropriate for differentiating minimal genomic variations, which makes this technique a valuable tool for the identification of isolates. PFGE was effective in showing epidemiological relationships among closely related isolates. Either technique allowed the discrimination of A. butzleri from A. cryaerophilus and A. skirrowii. When used together, s-AFLP and PFGE can be applied to determine taxonomic and epidemiological relationships among campylobacteria.