Like no the same fingerprint, there is also no the same cell in plant. Cells have the inherent heterogeneity. Different cells possess different cellular identity. Recent advances in the single-cell gene expression studies enable one to explore transcriptional regulation in dynamic development processes and highly heterogeneous cell populations. Here, to reveal the gene expression property of root in single-cell level, we performed the high-throughput single-cell RNA sequencing (scRNA-seq) assay. We found that the Arabidopsis root is highly heterogeneous. There are more than 24 clusters in the root cell populations. A series of new cluster-specific marker genes are identified. The spatial distribution of different cell types could reveal the hierarchy structure and reconstruct continuous differentiation trajectory of root cells. Thus, our studies identify certain cell types of root and present the intermediate states during root developmental process in the single-cell resolution.