A sensitive and selective biosensor was constructed for detection of Salmonella typhimurium carrying SSeC gene, based on covalently coupling of molecular beacons (MBs) stained with daunorubicins (DNR) to single-walled carbon nanotubes (SWNTs) through EDC/Sulfo-NHS chemistry. In the absence of target, the fluorescence of daunorubicin was fairly week as result of dual fluorescence quenching. On the contrary, the daunorubicin was competed from the beacon due to the target-induced formation of rigid structure between the loop structure of the MB and the target sequence, which resulted in a decrease in the effect of dual fluorescence quenching, thereby the fluorescence intensity increased substantially. The target quantum was achieved by fluorescence increment. The experimental results showed that the recovery of fluorescence of daunorubicin is proportion to the concentration of the target DNA with the range 0.2-0.7 μM and the low detection limit is 50 nM. The fluorescence intensity did not augment considerably when other Salmonella sps. were detected via the same method, which clearly displayed a high selectivity and specificity for the biosensor. Additionally, the real samples were also detected and their low detection limits were up to 105 CFU/mL. Consequently, the biosensor should be a potential alternative to the conventional detection ones and has great prospect in pathogenic microorganisms’ detection, clinical diagnosis and treatment.