Objectives Microplastic (MP) pollution is a global environmental concern due to their high production and improper management. Polypropylene (PP) and polyethylene (PE) are the most abundant MPs found in the coastal areas of South Korea. However, little information is available on the toxic effects of these environmentally relevant MPs on marine zooplankton. This study aimed to investigate the size- and shape-dependent toxicity of MPs in a marine rotifer. Methods In this study, intracellular reactive oxygen species (ROS) content and antioxidant enzyme activities (superoxide dismutase, SOD; catalase, CAT; and glutathione S-transferase, GST) were measured in the marine rotifer Brachionus koreanus after 24 h of exposure to small- and large-sized PP fragments and PE beads. Additionally, the transcriptional modulation of antioxidant enzyme-coding genes was examined using quantitative real-time polymerase chain reaction (qRT-PCR). Results Intracellular ROS level significantly increased with PP fragment in a size- and concentration-dependent manner, while it decreased with PE beads. Activities of SOD, CAT, and GST were elevated in most MP-exposed groups. PP fragments downregulated the mRNA expression of most antioxidant enzyme-coding genes, whereas PE beads upregulated their expression. Conclusions These findings suggest that PP and PE can induce oxidative stress and exert size- and shape-dependent effects on antioxidant systems. This study will enhance our understanding of molecular mechanisms through which environmentally relevant MPs impact marine zooplankton.