The ovipositor of apocritan Hymenoptera is an invaluable source of phylogenetically relevant characters, and our understanding of its functional morphology stands to enlighten us about parasitoid life history strategies. Although Ceraphronoidea is one of the most commonly collected Hymenoptera taxa with considerable economic importance, our knowledge about their natural history and phylogenetic relationships, both to other apocritan lineages and within the superfamily itself, is limited. As a first step towards revealing ceraphronoid natural diversity we describe the skeletomuscular system of the ceraphronoid ovipositor for the first time. Dissections and Confocal Laser Scanning Microscopy 3D media files were used to visualize the ovipositor complex and to develop character concepts. Morphological structures were described in natural language and then translated into a character-character state format, whose terminology was linked to phenotype-relevant ontologies. Four unique anatomical phenotypes were revealed: 1. The first valvifer (gonangulum) of the genus Trassedia is composed of two articulating sclerites, a condition present only in a few basal insect taxa. The bipartition of the first valvifer in Trassedia is most likely secondary and might allow more rapid oviposition. 2. Ceraphronoids, unlike other Hymenoptera, lack the retractor muscle of the terebra; instead the egg laying device is retracted by the seventh sternite. 3. Also unlike other Hymenoptera, the cordate apodeme and the anterior flange of the second valvifer are fused and compose one ridge that serves as the site of attachment for the dorsal and ventral T9-second valvifer muscles. Overall, the ceraphronoid ovipositor system is highly variable and can be described by discrete, distinguishable character states. However, these differences, despite their discrete nature, do not reflect the present classification of the superfamily and might represent parallelisms driven by host biology.