To investigate the application of DNA aptamers on detection and identification of food-borne pathogens， the whole-bacteria SELEX method was used to select single-stranded（ss） DNA aptamers with high binding affinity and specificity to Shigella flexneri. After multiple rounds of selection and counter-selection， 17 supposed aptamers were obtained from the enriched pool. Among them， 4 high-frequency aptamers were found to have significant affinities and specificities to S. flexneri. Further analysis indicated that F-1 and F-9 displayed higher affinities， and their binding affinity to S. flexneri were （51.3 ± 3.25） nmol/L and （42.6 ± 7.11） nmol/L， respectively. According to the Mfold software， the minimum free energy （dG） of F-1 and F-9 were determined to be -7.39 and -6.98 kcal/mol， respectively. The present study demonstrated the feasibility to detect S. flexneri by aptamers， which would pave the way for its application in diagnosing food-borne pathogens.