The pygidium is a terminal part of the annelid body that is considered non-homologous to body segments. Despite the high level of morphological diversity, the internal morphology of the pygidial region is very poorly studied. Recent research revealed that in some errant annelids the pygidium possesses complex musculature and innervation. To provide new data for the comparative analysis of pygidial organization, the musculature and innervation in the pygidial region in five annelid species belonging to the order Eunicida were studied using phalloidin labeling, immunohistochemistry and confocal scanning microscopy. In all studied species the pygidial musculature consists of a circular or horseshoe-shaped muscle. The pygidial innervation comprises two pairs of main longitudinal nerves and paired circumpigidial nerves. The single pair of longitudinal nerves in Ophryotrocha irinae may be regarded as a secondary loss. In Schistomeringos japonica a small terminal commissure between longitudinal nerves was found. The finding of numerous receptor cell endings in the surface of the pygidium suggests its important sensory function. Comparison with Phyllodocida demonstrates the high level of similarities in the pygidial organization and the loss of the terminal commissure in Eunicida.