Abstract: CdSe quantum dots (QDs) were synthesized in aqueous solution using mono-(6-mercapto)--cyclodextrin as stabilizer in this paper. And the purification of CdSe/CD QDs with different solvents in a series of proportions was investigated systematically. The fluorescence properties of CdSe/CD QDs were characterized by fluorescence microscope and fluorescence spectroscopy. In addition, the application of CdSe/CD QDs in bacteria marking and molecular recognition was also studied. The results showed that the purification with twice volume acetonitrile was best. And CdSe/CD QDs can be used not only to mark E. coli and Bacillus subtilis, but also quantitatively detect vitamin B1, vitamin C, 6-mercaptopurine, 6-mercaptopurine ribonucleoside, 4-amino-6-hydroxy-2- mercaptoprimidine.