Bacillus amyloliquefaciens containing intracellularly biosynthesized cadmium selenide (CdSe) quantum dots (QDs) was used as a fluorescent bioprobe. Several parameters in the QD biosynthesis process were systematically optimized. The optimized protocol for producing high-quality CdSe QDs in B. amyloliquefaciens features mild synthetic conditions, good reproducibility, short reaction time and high yield. This process shows promise for the mass production of QDs by bacterial matrices. The resultant fluorescent B. amyloliquefaciens containing intracellular CdSe QDs was used as a bioprobe for the simple detection of copper (II) ions in blood plasma. The selective permeability of the bacterial cell membrane along with the protection provided by a protein envelope on the QD surface prevented interference by other components of blood plasma, resulting in the accurate determination of Cu2+. Using the copper addition method, the content of Cu2+ in human blood plasma samples was determined to be 15.6-18.5 mu mol/L, consistent with atomic absorption spectroscopy results. The technique developed here shows potential for the simple determination of Cu2+ in plasma with excellent selectivity and good sensitivity.