The extracellular matrix (ECM) is a dynamic system whose innovations have helped facilitate morphological evolution in animals. ECM components provide structure and support and also direct tissue differentiation and cellular communication. An ECM component of interest in vertebrates is hyaluronan (HA), a glycosaminoglycan (GAG) that aids in the development of the heart, brain, and jaw. Likewise, of interest in invertebrates is chitin, which is involved in the formation of the exoskeleton and digestive tract. Despite HA and chitin’s different functions, they are thought to be duplicates of a common ancestral glycosyltransferase gene. Previous studies have identified three HA synthase (Has) genes unique to vertebrates. Several vertebrates maintain both HA and chitin. This led to the question of how HA and chitin play a role in the development of the vertebrate body plan, by examining organisms that lack morphological structures most vertebrates share. We decided to look at Has genes in sea lamprey, Petromyzon marinus, a jawless vertebrate that diverged about 500 million years ago. In situ hybridization and histochemical staining led to the discovery of five Has genes in lamprey. The lamprey transcriptome revealed three type-II chitin synthase (Chs) genes. Has and Chs expression patterns in lamprey are comparable to that of other vertebrates, with few notable exceptions with Chs. We were next interested in the interplay between HA and chitin during development, doing loss-of-function experiments in Xenopus laevis for Has and Chs genes. Our findings suggest that ancestral gene duplication events in Has and Chs genes predate the divergence of vertebrate and invertebrate chordates. We also suggest that the evolution of the vertebrate body plan involved recruiting the novel GAG HA and the progressive loss of chitin.