Systematical descriptions of phytoliths from rice species in East Asia are scarce. In order to investigate the relationship among diversity of phytolith morphology, taxonomy and genome, comparative research on phytolith morphology of the wild and domesticated rice species is first performed on the basis of statistics and cluster analysis. All morphological parameters were measured at 500× magnification using a Zeiss light microscope. 3-D plots and cluster analysis are performed by SPSS 10.0 software. The leaves and inflorescences of domesticated and wild rice contain a great diversity of phytolith types including long cells, short cells, bulliform cells, hair cells, irregular epidermal cells, mesophyll and vascular tissues. Comparative research on phytolith morphology demonstrates that most overlap occurs among long cells, short cells, bulliform cells, hair cells and vascular tissues at the species level. Rondels, crosses, long cells, hair cells, parallepipedal bulliform cells, tracheid and vascular tissue exhibit no taxonomical value. Complex saddles and irregular epidermal phytoliths might be diagnostic to the rice species that had not been described before. Further comparative research on the morphological features of three phytolith types from the wild and domesticated rice species has confirmed that double-peaked glume cells measurements can separate domesticated Oryza species from wild ones successfully. Hierarchical cluster analysis on all morphological parameters of bilobates, cuneiform bulliform cells and double-peaked glume cells strongly demonstrates that phytolith assemblage appears to be under genetic control and therefore reflect taxonomical significance. The results are significant for plant physiology, rice cultivation and environmental archaeology.