During synapsid evolution, postdentary elements in the reptilian jaw transitioned into the middle ear of mammals. Though this astounding change is well documented in the fossil record, questions regarding the developmental sequence that drove the ossicular transition still remain. At birth, modern marsupials possess a very reptilian jaw joint with functional articulation between the articular and quadrate. These elements will later become the malleus and incus, respectively, of the middle ear. This entire transition occurs postnatally, and represents a natural system for comparison with the fossil record. We utilized Monodelphis domestica as a model organism, and traced the development of ossicular structures as they separate from the jaw and fully incorporate into the middle ear. Micro-CT scans throughout development and three-dimensional reconstructions show decreasing size and rearward movement of ossicles are false illusions created by continued growth and expansion of the surrounding skull elements. Cryosections and immunohistochemistry reveal separation of Meckel’s cartilage from the malleus occurs at postnatal day 20 and is facilitated by apoptosis. Additionally, laser capture microscopy and RNA sequencing identify differential gene expression at the time of separation and breakdown of the connecting Meckel’s cartilage. The morphological changes are facilitated by an upregulation of cartilage resorption genes paired with simultaneous downregulation of proliferative genes. Finally, marsupial developmental stages were compared with the known fossil record of early mammals exhibiting transitional forms of the definitive mammalian middle ear in order to resolve the question, in this instance, of whether ontogeny is truly recapitulating phylogeny.