Introduction: Tardigrades are an ancient lineage of microinvertebrates with a unique metameric pattern consisting of a head and four lobopodal leg-bearing segments. While their close relationship to Onychophora and Arthropoda is well established, many questions remain about the structure and origin of the tardigrade metameric pattern. For example, the relationship of the tardigrade head to that of Arthropoda and Onychophora remains a contentious issue. One source of contention stems from disagreement about the structure of the tardigrade brain. The availability of developmental tools for the tardigrade Hypsibius dujardini give this species the potential to clarify questions regarding the relationship of tardigrade segmental patterns to those in Arthropoda and Onychophora. Here we investigate the nervous system, muscle system, and cuticle anatomy of H. dujardini using high-resolution microscopy methods. Results: We characterized nervous system anatomy of H. dujardini using a combination of anti-β -tubulin staining and DAPI staining and muscle system anatomy using phalloidin staining. We identified several brain lobes: paired outer lobes, paired inner lobes, and a single horseshoe-shaped ventral lobe. We also characterized similarities and differences in the nervous system and muscle system anatomy of the four body segments. Based on these, we detect distinct morphological identities for each segment in this species.