Unlike eutherian males, pairing of the sex chromosomes in marsupial males during the first meiotic prophase is not mediated by a synaptonemal complex. Instead, a specific structure, the dense plate, develops during pachytene between the sex chromosomes. We have investigated the development and structural nature of this asynaptic association in males of the marsupial species Thylamys elegans by means of immunolabelling and electron microscopy techniques. Our results show that the behaviour of male marsupial sex chromosomes during first meiotic prophase is complex, involving modifications of their structure and/or composition. Pairing of the sex chromosomes and formation of the dense plate take place in mid pachytene, paralleling morphological changes in the sex chromosomal axial elements. Components of the central element of the synaptonemal complex were not found in the sex body, in agreement with ultrastructural studies that reported the absence of a canonical tripartite synaptonemal complex between male marsupial sex chromosomes. Interestingly, the dense plate is labelled with antibodies against the SCP3 protein of the lateral elements of the synaptonemal complex. Moreover, as sex chromosome axial elements decrease in mass throughout mid-late pachytene, the dense plate increases, suggesting that material moves from the axial elements to the dense plate. Additionally, both sex chromosome axial elements and the dense plate have proteins that are specifically phosphorylated, as revealed by their labelling with the MPM-2 antibody, indicating that they undergo a chromosome-specific regulation process throughout first meiotic prophase. We propose that the unique modifications of the composition and structure of the axial elements of the sex chromosomes in meiotic prophase may result in the prescription of synaptonemal complex formation between male marsupial sex chromosomes, where the dense plate is an extension of the axial elements of sex chromosomes. This replaces synapsis to maintain X and Y association during first meiotic prophase.