The vertebrate mesoderm is divided into several compartments: the cranial mesoderm, the axial mesoderm (prechordal plate, notochord), the paraxial mesoderm which is segmented into somites, and the lateral mesoderm. The latter is involved in the formation of several vertebrate-specific structures, including a closed circulatory system, a chambered heart, or paired appendages (limbs/fins) in jawed vertebrates. The notochord and somites are ancestral structures in chordates. On the other hand, the origin of the lateral mesoderm, and the evolution of the structures derived from it, remain enigmatic. We propose to decipher the evolutionary and developmental trajectory of the lateral mesoderm using two model species having a key phylogenetic position: the cephalochordate amphioxus and the lamprey, a jawless vertebrate, through a detailed morphological description paralleled by a single-cell transcriptional analysis approach.