The DNA molecular of the exotic microorganism Bacillus subtilis 38 (B38, a mutant species of Bacillus subtilis) was used labelled by a fluorescent dye, DAPI (4', 6-Diamidino-2-Phenylindole), to monitor the microorganism growth during the process of soil remediation by bioaugmentation technique. By optimizing the DAPI concentration and the dilution ratio of the bacterial suspension, an ideal DAPI concentrations of 0.1 μg/mL and a bacterial suspension dilution fold of 10¹⁰ were applied, and the appropriate fluorescence intensity and cell dispersity for the accurate fluorescent dot counting were obtained. The quantitative changes of B38 in 60 days soil remediation was monitored under the optimized conditions. The results showed that the numbers of B38 in soil increased obviously, and then reached an equilibrium concentration of (1.05±0.01)×10¹⁰ cells/mL. The equilibrium concentration was as high as 3orders of magnitude of the initial dosage. Thus, DAPI labelled fluorescent tracing technique was a convenient and effective approach to monitor the growth and reproduction of exotic microorganism.