Clam shrimps have been recognized as a key group for the study of reproductive system evolution, owing to the diversity of sexual systems in extant members. However, there are comparatively little data on fossil taxa. In this study, we reveal the sexual system of the Early Cretaceous clam shrimp Eosestheria middendorfii (Yixian Formation, China). This is the first study that restricts the analysis to a single cohort, minimizing the otherwise considerable impact of ecophenotypic variation within this species. In addition, the presence of egg clutches, which identifies some individuals as either female or hermaphroditic, serves as an independent indicator for sex prior to the statistical treatment of the data. Obligate sexuality (‘dioecy’) is the inferred reproductive system for E. middendorfii and sexual dimorphism accounts for about 10% of the adult shape variation. Carapace shape variation resulting from malformation and deformation is more pronounced than the underlying sexual dimorphism. Subtle sexual dimorphism, smaller and slightly more elongate females, lateral egg clutches, and egg diameters of about 140 μm indicate that E. middendorfii is closely allied with the extant family Cyzicidae.