Orthonectida is a small group of parasites, which, according to recent studies, may be phylogenetically close to Annelida. Here, we describe the musculature and serotonin-like immunoreactive (SLIR) nervous system of male adults of Intoshia linei (Orthonectida) using immunohistochemistry and confocal laser scanning microscopy. The whole muscular system consists of four outer longitudinal and eight pairs of inner semicircular muscle fibres. Immunohistochemistry revealed six serotonin-like cells at the anterior part of the body, and two backward lateral longitudinal nerves, merging at the posterior end. Compared to females, the organization of the nervous system is modified and its progenetic origin seems unlikely. The general neuromuscular organization corresponds to the pattern of small-sized annelids, suggesting their possible phylogenetic affinity. Free-living males and females of the orthonectid I. linei may present a good example of a highly simplified Bilaterian with fully functioning nervous and muscular systems. This simplicity is secondary and is caused by two factors—the parasitic life style and miniaturization of free-living sexual stages.