Most freshwater cladocerans produce resting eggs in their life cycle under harsh conditions. The hatchings from those eggs not only impact cladoceran population and community succession but also link to the long-term shifts in cladoceran genetic structure over time. DNA extraction from resting eggs became a key to enable genetic analyses of past cladoceran populations. In order to find a suitable method for extracting high quality genomic DNA from Cladocera resting eggs, the Ultra-Sep Beads method and chloroform isoamyl alcohol method were used to extract DNA from resting eggs of Daphnia galeata in Liuxihe Reservoir. The success rate and concentration of the DNA extracted by Ultra-Sep Beads method were higher than those from chloroform isoamyl alcohol method. The success rate and concentration of the DNA extracted by Ultra-Sep Beads method reach to 65.0% and 28.37 ± 2.56 ng/μl, while 27.5% and 14.25 ± 1.84 ng/μl by chloroform isoamyl alcohol method, respectively. The comparative study exhibited that Ultra-Sep Beads method is an effective method of DNA extraction for resting egg of Cladocera in the sediment, given its simple and fast process and avoiding using chloroform.