Planarians have regenerative ability made possible by pluripotent stem cells referred to as neoblasts. Classical ultrastructural studies have indicated that stem cells can be distinguished by a unique cytoplasmic structure known as the chromatoid body and their undifferentiated features, and they are specifically eliminated by X-ray irradiation. Recently, by using fluorescence activated cell sorting (FACS), planarian cells were separated into two X-ray-sensitive fractions (X1 and X2) and an X-ray-insensitive fraction (XIS) according to DNA content and cytoplasmic size. Here we analyzed the fractionated cells by transmission electron microscopy (TEM). First, we found that both undifferentiated cells (stem cells) and regenerative cells (differentiating cells) were concentrated in the X1 fraction containing the S/G2/M phase cells. The regenerative cells were considered to be committed stem cells or progenitor cells, suggesting that some stem cells may maintain proliferative ability even after cell fate-commitment. Second, we succeeded in identifying a new type of stem cells, which were small in size with few chromatoid bodies and a heterochromatin-rich nucleus. Interestingly, they were concentrated in the X2 fraction, containing G0/G1 phase cells. These results suggest that planarian stem cells are not homogeneous, but may consist of heterogeneous populations, like mammalian stem cells.