The HMG box containing protein (HBP) has a high mobility group domain and involved in the regulation of proliferation and differentiation of tissues. We screened HBP2 in glioblastoma using Suppression Subtractive Hybridization (SSH) and isolated human spermatogonial stem cell‐like cells (hSSC‐like cells) derived from patients of nonobstructive azoospermia (NOA). Expression of HBP2 was analyzed by RT‐PCR in undifferentiated stem cells (human Embryonic Stem Cells, hSSC‐like cells 2P) and spontaneous differentiated stem cells (hSSC‐like cells 4P). It was overexpressed in hESC and hSSC‐like cells 2P but not in hSSC‐like cells 4P. Also, the expression level of HBP2 was downregulated in colon tumor tissues compared to normal tissues. Specifically in synchronized WI‐38 cells, HBP2 was highly upregulated until the G1 phase of the cell cycle and gradually decreased during the S phase. Our results suggest that HBP2 was downregulated during the spontaneous differentiation of hSSC‐like cells. HBP2 was differently expressed in colon tissues and was related to G1‐progression in WI‐38 cells. It may play a role in the maintenance of an undifferentiated hSSC‐like cell state and transits from G1 to S in WI‐38 cells. This research was important that it identified a biomarker for an undifferentiated state of hSSC‐like cells and characterized its involvement to arrest during cell cycle in colon cancer.