Biological interactions are rarely preserved in the fossil record and where they do occur, are often difficult to discern. Therefore, the evolution of sexual systems over geologic time in animals has been difficult to investigate. The reproductively labile Spinicaudata ('clam shrimp') are a model clade for the study of sexual systems, containing dioecious (males and females), androdioecious (males and hermaphrodites) and self-fertilizing hermaphrodites. Herein we present a methodology in which mating systems can be inferred by the quantification of carapace shape differences attributable to sexual dimorphism in fossil specimens. We develop our methodology by comparing the carapaces of six species from two families of extant Spinicaudatans using eigenshape analyses. Sexual dimorphism was successfully quantified using morphometric techniques combined with discriminant analyses, correctly identifying males and females/hermaphrodites 92% of the time in extant taxa. Thirty-four specimens of the Jurassic clam shrimp Carapacetheria disgragaris were analyzed utilizing the methods developed with extant species. From these fossil data, we were able to detect two distinct carapace shapes and assign 100% of individuals to either shape. The mean carapace shapes of the fossil specimens fit well with the average outlines for males and females in the extant species, enabling us to calculate a sex ratio of 51:49 males:females and thereby assign the sexual system of dioecy. This study begins to successfully utilize the fossil record of the Spinicaudata to elucidate ancient sexual systems, which will likely have far reaching implications for our understanding of the evolutionary dynamics of sexual systems over geologic timescales.