The production of low numbers of offspring that exhibit a mixture of male and female traits (termed “intersexes”) is commonly reported for crustaceans. The production of intersexes has been ascribed to both genetic and non-genetic (e.g., parasitic infections and environmental pollutants) causes. Herein we report on two observed types of intersexes in the clam shrimp Eulimnadia texana: (1) a “morphological” intersex, possessing secondary male characteristics (e.g., claspers) and a clear egg-producing gonad, and (2) a “histological” intersex, possessing primarily male traits (e.g., male secondary sexual characters and male gamete production) but also producing low levels of abortive female gametes. We propose that these intersexes are likely the products of low frequencies of crossing over between the sex determining chromosomes that result in the array of observed mixed sexual phenotypes. Additionally, we suggest that the low-level production of intersexes, combined with the ephemeral nature of the habitats occupied by these shrimp, may explain the preponderance of the rare mating system androdioecy (mixtures of males and hermaphrodites) found in these clam shrimp, and possibly branchiopods more generally.