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During metamorphosis, the central nervous system (CNS) of holometabolous insects undergoes complex structural and allometric changes. In exceptional cases, the CNS can follow an extreme path of cell reduction, such as the denucleation of neurons in species of the parasitic wasp genus Megaphragma (Hymenoptera: Trichogrammatidae). Studying the metamorphosis of the CNS in one of the smallest wasps, Megaphragma viggianii, we obtained the first data on the morphological and volumetric changes in its CNS during pupal development with emphasis on nucleus lysis in the neurons. We showed that the absolute and relative volumes of the brain during pupal development decrease by a factor of 5, due to the decreasing cell body rind. Our analysis of the cellular ultrastructure of the pupal brain showed that most (up to 97%) of the loss of neuron nuclei occurs at the stage of the pharate adult. Despite the cell body rind loss, the volume of the neuropilar part of the brain remains virtually unchanged during pupal development. The first signs of the lysis of neuron nuclei are observed in the red-eyed pupa. In the black-eyed pupa, the number of lysis foci increases considerably, many organelles are destroyed, and the degree of chromatin compaction noticeably increases. Elucidation of the molecular basis of denucleation, mechanisms that provide for anucleate neurons functioning, and principles of the organization of neuronal circuits in a nearly anucleate brain is of fundamental value for neuroscience and require further comprehensive studies. This study was supported by the Russian Science Foundation (project no. 22-74-10008).