An atlas of the naupliar development of the cirripede Balanus improvisus Darwin, 1854 using scanning electron microscopy (SEM) is provided. Existing spikes on the hindbody increase in number with each moult and are an applicable character for identification of the different nauplius stages, as is the setation pattern of the first antennae. The naupliar musculature of B. improvisus was stained with phalloidin to visualise F-actin, followed by analysis using confocal laser scanning microscopy (CLSM) with subsequent application of 3D imaging software. The larval musculature is already fully established in the first nauplius stage and remains largely unchanged during all the six nauplius stages. The musculature associated with the feeding apparatus is highly elaborated and the labrum possesses lateral muscles and distal F-actin-positive structures. The alimentary tract is entirely surrounded by circular muscles. The extrinsic limb musculature comprises muscles originating from the dorsal and the ventral sides of the head shield, respectively. The hindbody shows very prominent postero-lateral muscles that insert on the dorso-lateral side of the head shield and bend towards ventro-posterior. We conclude that the key features of the naupliar gross anatomy and muscular architecture of B. improvisus are important characters for phylogenetic inferences if analysed in a comparative evolutionary framework.