In this paper, we investigated a novel imaging technique that employed molecular beacons capable of binding specifically to in vivo targets such as protein and mRNA. We used capillary electrophoresis to select aptamers, i.e. high affinity oligonucleotides specific for a particular target, which were subsequently incorporated into the loop section of molecular beacons for target recognition. The results verified the advantages of using molecular beacons together with near-infrared fluorescence, in terms of improving probe specificity and reducing autofluorescence for in vivo imaging. It was also demonstrated that capillary electrophoresis was able to isolate MB probe aptamers with high efficiency.