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 egg stage. One well studied large branchiopod is the clam shrimp Eulimnadia texana, an androdioecious species with populations comprised of males and self-compatible hermaphrodites. Likely due to the harsh environments in which the eggs are found, e.g., dry areas with high heat and high irradiation, extraction of DNA from individual eggs for genetic analyses can be problematic. Here we report a number of modifications that we have tested allowing for increased efficiency and success in extracting high quality DNA from the eggs, nauplii, and adults of E. texana that may prove useful for similar studies of other species of large branchiopods.