Water-soluble, biologically compatible CdSe quantum dots (QDs) with L-cysteine as capping agent were synthesized in aqueous medium. Fluorescence (FL) spectra, absorption spectra, and transmission electron microscopy studies showed that both the molar ratio of Se/Cd and the reaction time are the determining factors for the size distribution of CdSe/L-Cysteine QDs. The interaction of QDs bioconjugated to bovine serum albumin (BSA) was also studied by absorption and FL titration experiments. With addition of QDs, the FL intensity of BSA was largely quenched, which can be explained by static mechanism. However, when BSA was added to the solution of QDs, FL intensity of QDs was faintly enhanced at first and then quenched. Lysozyme could change the Escherichia coli (E. coli) membrane fluidity and permeability by FL polarimetry. Fluorescent imaging suggested that QDs can be designed as a probe to label the E. coli cell. These results suggested CdSe/L-Cysteine QDs can be used as a probe for labeling biological molecule and bacteria cell.