Objective To compared the ratios of fluorescence labeling cells to the lin( － ) c-kit( + ) Sca-1 + ( LSK)stem cells from the five transgenic mouse lines，selected the mouse lines of totally fluorescence labeled，for tracking the hematopoietic stem cells and in vivo fluorescence imaging analysis． Methods The expressions of the fluorescent protein in vivo were observed under in vivo fluorescence imaging system，the expression of those genes in the stem cells were investigated with flow cytometry． Results The fluorescent protein was expressed in most tissues in the five transgenic mice． The fluorescent protein expressions were observed in almost all LSK stem cells of C57BL /6J-TgN( CAG-DsRed-1) ZLFILAS and C57BL /6J-TgN ( CAG-EGFP-1 ) ZLFILAS． Conclusions Two transgenic mouse lines were indicated in which LSK stem cells were marked completely by red or green fluorescence protein separately，suggesting the two mouse lines may be useful tools for in vivo tracking the hematopoietic stem cells．