4’,6-diamidino-2-phenylindole (DAPI), as one of specific DNA fluorescent dyes, is widely used in fluorescence microscopic observation of various biological cells. However, there is still lack of a systematic characterization of different tissues response to DAPI staining in plant. In this study, using the model plant Arabidopsis thaliana, we explored the differential responses to DAPI staining in various tissues. Firstly, we generated a stable nucleus-targeted transgenic plant UBQ10∶BAG5-eYFP. The results showed that only the epidermal cells and mesophyll cells can be stained by DAPI in living plant. Compared with chloroplast, the DNA in mitochondria is very sensitive to DAPI staining, displaying a good co-localization between the fluorescence of DAPI and mitochondrial marker CoxIV-RFP. After fixed with paraformaldehyde, the root meristem zone and stomatal guard cells can be stained by DAPI. These results indicated that different tissues have great differences when being stained with DAPI in Arabidopsis. The leaf epidermal cells and mesophyll cells would be good models for studying the function of nucleus in living plant.