The systematic position of the Orthonectida remains enigmatic. According to a classical point of view, they are placed together with Dicyemida in the phylum Mesozoa. Traditionally, orthonectids are regarded as rather primitive organisms, lacking digestive, muscular, and nervous systems. Here, using confocal laser scanning microscopy (CLSM) and immunohistochemical methods, we describe the musculature and serotoninergic nervous system of female adults of Intoshia linei (Orthonectida). The whole muscular system consists of 4 longitudinal and 9–11 circular muscle cells. The general muscular topography corresponds to the typical pattern for small-sized annelids or flatworms. Immunohistochemistry reveals six serotonin-like cells, which form part of a small nervous system comprising only 10–12 total cells based on nuclear counts. This is the first finding of a serotoninergic nervous system in orthonectids. Our analysis of muscular and neural organization in Orthonectida reveals significant differences from Diciemyda and aligns it more closely with the Lophotrochozoa.