Abstract: We have developed a method for sorting specific cells in plant. Here, WER::GFP transgenic lines in Arabidopsis thaliana were as the experimental material; laser scanning confocal microscopy was used to identify the expression location of GFP; enzymatic digestion was applied for preparation of root tip protoplasts; fluorescence activated cell sorting (FACS) was applied to collect GFP positive cells; and then the total RNA was extracted from these cells. The results showed that only the early developmental non-root hair cells in the root epidermis express GFP in Wer::GFP transgenic lines; larger number of root tip protoplasts were obtained by using enzymatic digestion; and then GFP positive cells were collected successfully by FACS. The RNA extracted from these specific cells can be used for gene expression profiling. The method for sorting specific cells had been established successfully.