Vibrio alginolyticus is an opportunistic pathogen that can infect many aquatic animals and cause economical losses to aquaculture and the food industry. Therefore, sensitive and rapid detection of V . alginolyticus is urgently needed. In the present paper, three aptamers were proved to have good specificity towards inactivated V . alginolyticus , and they could distinguish inactivated V . alginolyticus from inactivated Vibrio harveyi , Vibrio parahaemolyticus , Vibrio anguillarum , Edwardsiella tarda , Aeromonas hydrophila and Escherichia coli . Incubating heat- and formaldehyde-treated cells with aptamers #7, #8, and #23, washes with binding buffer, heat-induced release of bound aptamers, and application of the polymerase chain reaction to amplify the aptamers allowed the detection of 10, 10 and 10 3 cells/ml, respectively. Aptamer #8 had good affinity with both live and inactivated V . alginolyticus . The combination of aptamers #8 and #7, or aptamers #8 and #23, could distinguish live V . alginolyticus from inactivated V . alginolyticus based on their different affinities with the microorganism. The putative secondary structures were determined for these aptamers using software RNAstructure 5.3 and the affinity constants (Kds) 28.39 ± 11.46, 12.82 ± 6.00 and 46.89 ± 15.87 nM, were calculated respectively by employing their saturation curves. The results demonstrated that an aptamer-based method can be used for the detection of V . alginolyticus .