Cranial base synchondrosis lacks PTHrP+ column-forming chondrocytes in the resting zone. PTHrP+ chondrocytes are present both in the femoral growth plate and cranial base synchondrosis, which are generally characterized by their slow-cycling nature. Our cell-lineage analysis using Pthrp-creER; R26RtdTomato mice reveals that PTHrP+ chondrocytes in the synchondrosis fail to form columnar chondrocytes. Thus, PTHrP+ chondrocytes do not possess the characteristics of skeletal stem cells in the synchondrosis, highlighting functional differences between skeletal stem cells and their niches in two classes of endochondral bones—the cranial base and long bone. Red cells: mCherry+, tdTomato+, Green cells: EdU+, Yellow cells: mCherry+; EdU+. R: resting zone, P: proliferating zone, H: hypertrophic zone, PS: primary spongiosa, M: metaphyseal bone.