Conchostracan shrimp, along with most large branchiopod crustaceans inhabiting ephemeral ponds, are well adapted to their highly unpredictable habitat with a life cycle that includes a short-lived adult stage and a long-lived, desiccation-resistant cyst stage. One well studied large branchiopod is the clam shrimp Eulimnadia texana, an androdioecious species with populations comprised of males and self-compatible hermaphrodites. The hermaphrodites produce clutches of cysts which usually require a drying period before subsequent hatching. These encysted embryos represent a rich source of information for analyses of genotypic structure within a given population. In addition, single clutches of cysts contain genetic information from both the maternal and paternal parents, if the embryos are the product of outcrossing with a male and not complete self-fertilization. Likely due to the harsh environments in which the cysts are found (e.g., dry areas with high heat and high irradiation) we have found the extraction of their DNA to be somewhat problematic. Here we present the results of various methodologies allowing for reproducible extraction of high quality DNA from the cysts, nauplii, and adults of E. texana that may prove useful for similar studies of other species of large branchiopods.