Background: The monitoring of pathogens of fishery auction markets is important to obtain safe fishery products regarding hygiene and sanitation. In this study, aerobic, coliform, Escherichia coli, and Vibrio cholerae were monitored in the fishery products and environmental samples obtained from fishery auction markets. Methods: The fishery products (flounder, octopus, skate, rock cod, sea bass, snail, monkfish, flatfish, comb pen shell, corb shell, conger eel, hairtail, croaker, and pilchard) were placed in filter bags, and the environmental samples (samples from the water tanks at the fishery auction markets, seawater from the fishery distribution vehicles, ice from wooden or plastic boxes, and surface samples from wooden and plastic boxes used for fish storage) were collected. Aerobic bacteria, E. coli, and coliform in the samples were enumerated on aerobic count plates and E. coli/coliform count plates, respectively. For V. cholerae O1 and V. cholerae non-O1 quantification, most probable number (MPN)-PCR analysis was performed. Results: Aerobic and coliform bacteria were detected in most samples, but E. coli was not detected. Wooden boxes were contaminated with high levels of aerobic and coliform bacteria in all seasons (spring, summer, and fall). During fall, V. cholerae non-O1 were detected in snails, hairtails, croakers, flatfishes, pilchards, plastic boxes, and water samples. Conclusions: These results indicate an increased prevalence of V. cholerae contamination in fishery products in fall, including food contact samples, which can be vehicles for cross-contamination.