Marine zooplankton play an important role in regulating the global biogeochemical cycle and serve as the key link between lower and higher trophic levels. Considering their ecological significance, understanding their evolutionary success under ocean acidification (OA) conditions is useful for ecosystem management. Changes in the transcriptome driven by DNA methylation in response to rapid environmental stress give marine animals the ability to create phenotypic plasticity. It is currently unknown, however, whether DNA methylation’s role in phenotypic plasticity applies to zooplankton (microscopic organisms) with small genomes. This is due to technological limitations in non-model species including difficulty accommodating small sample size population analyses. The purpose of the present studies was to investigate whether epigenetic changes may be key mechanisms in zooplankton for enhancing their transgenerational plasticity in response to environmental stressors.