Adult parasitic barnacles significantly differ from their free-living relatives. This leads to uncertainty in the phylogenetic interrelationships even at the family-level, particularly for the former Lernaeodiscidae. This family was abolished based on molecular data, however, the morphological description for lernaeodiscids remains incomplete. Here we describe a morphology of Lernaeodiscus rybakovi parasitizing the porcelain crab Pachycheles stevensii, using a variety of methods. The externa's lacunar and muscular systems are “Kentrogonida”-type in general, but exhibit notable deviations, including an atypical mantle opening formed partly by the visceral mass and a distinct dorso-ventral bridge. The interna displays a previously undescribed organization: a prominent main trunk giving rise to flattened primary branches and tubular secondary rootlets. Muscular fibers are absent in the interna; only sparse actin filaments are present, suggesting alternative mechanisms of nutrient transport. Two invasive rootlet types—goblet-shaped organs and neuropil rootlets—interact with host nervous tissue, and their ultrastructure differs from that of other rhizocephalan families. Additionally, we describe an aberrant trophic rootlet filled with concentric extracellular matrix layers, likely reflecting localised misregulation of cuticle production. Our findings, together with molecular evidence, suggest that Lernaeodiscus may represent an independent lineage, warranting exclusion from Peltogastridae and possibly reinstatement of Lernaeodiscidae. Broader sampling and multigene phylogeny are needed to clarify its rank and composition.