Vertebrates are defined by the presence of the neural crest. These cells contribute to the increased complexity of vertebrates relative to non-vertebrate chordates. It is widely accepted that an increase in vertebrate complexity is also related to gene duplications that occurred at the base of vertebrates and may be related to the origin of the neural crest. Study of the development of one neural crest derivative, pharyngeal cartilage, in the lamprey and comparison to chondrogenesis in other chordates may provide clues regarding acquisition of a chondrogenic fate by the neural crest. The transcription factor Sox9 is thr product of a SoxE gene (Col2a1) that regulates expression of Type II collagenin development of vertebrate cartilage. Duplication of the ancestral SoxE transcription factor into the three SoxE genes present in vertebrates might have been important in partitioning the chondrogenic neural crest role of Sox9. In this review, I discuss evidence that duplicated SoxE genes might have been key in the evolution of chondrogenic neural crest. The recent identification of duplicated SoxE genes, and identification of two Type II collagen genes in lamprey, coupled with their expression in branchial arches suggested ancient regulation of chondrogenesis by a SoxE gene. Examination of SoxE and Type II collagen expression in the developing lamprey branchial arches shows SoxE genes are expressed in developing branchial arch cartilage and Col2a1 genes are expressed in surrounding mesenchymal cells. Lack of cellular co-expression of SoxE genes with Col2a1 suggests additional steps might have been required for direct regulation of Col2a1 by Sox9 in jawed vertebrates.