The microstructure of type I collagen, consisting of alternating gap and overlap regions with a characteristic D period of approximately 67 nm, enables multifunctionalities of collagen fibrils in different tissues. Implementing near-surface dynamic and static nanoindentation techniques with atomic force microscope, we reveal mechanical heterogeneity along the axial direction of a single isolated collagen fibril from tendon and show that, within the D period, the gap and overlap regions have significantly different elastic and energy dissipation properties, correlating the significantly different molecular structures in these two regions. We further show that such subfibrillar heterogeneity holds in collagen fibrils inside bone and might be intrinsically related to the excellent energy dissipation performance of bone.