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Traditional morphological identification difficulties, such as phenotypic plasticity, misidentification of cryptic species, and larval stage species, can be compensated for by using DNA analysis techniques, such as DNA barcoding, in surveying zooplankton populations, including species identification. Recently, the rapid development of DNA sequencing techniques has allowed DNA-based community analysis not only for zooplankton assemblages in various aquatic ecosystems but also for the gut contents of zooplankton that are limited by conventional methods such as visual and microscopic identification. Therefore, the application of DNA sequencing can help understand biological interactions through the analysis of zooplankton food sources. The present paper introduces the major DNA-based approaches in zooplankton research topics, including taxonomic approaches by DNA barcoding, community-level approaches by metabarcoding, and gut content analyses, summarizes the analysis methods, and finally suggests the methodological topics that need to be considered for future applications.