Cartilage is composed of chondrocytes of distinct embryonic origins, mesoderm and neural crest (NC), but the degree of similarity between chondrocytes derived from the distinct embryonic lineages is still debatable. During endochondral ossification, two types of chondrocytes differentiate in the head and limb skeletons, immature chondrocytes (IMM) and mature chondrocytes (MAT), so both cell types can derive from the mesoderm or the neural crest. To test the hypothesis that the transcriptomes of mesoderm- and NC-derived chondrocytes are conserved, LCM was used to isolate IMM and MAT from two endochondral bones in the chick limb and head, the humerus and the ceratobranchial, which are mesoderm- and NC-derived, respectively. Venn diagram analyses revealed that the humerus and ceratobranchial transcriptomes show a high degree of conservation. Although they exhibit some differences in gene expression, the fundamental set of genes driving cartilage differentiation including SOX9, COL2A1, and COL10A1 was generally conserved. Indeed, some enriched biological processes in genes shared between the humerus and the ceratobranchial are related to skeletal cell differentiation. In contrast, GO analyses revealed that enriched biological processes in the humerus are related to limb/forelimb morphogenesis whereas enriched terms in the ceratobranchial are related to neural crest-dependent processes. Together these results suggest that the molecular program driving cartilage differentiation is conserved regardless of embryonic origin or location in the body. Adding more clades into these transcriptomic comparisons can make this conclusion more robust and might provide novel insights into mechanisms of differentiation and evolutionary origins of cartilage.