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Microplastics (MPs) have become global environmental concern. However, the effects of environmental concentrations of MPs, singly or in combination with organic pollutants, on the early development of marine fish remain unclear. In this study, fertilized eggs of marine medaka (Oryzias melastigma) were exposed to polystyrene MPs (0, 2, 20, 200 μg/L) and/or phenanthrene (Phe, 50 μg/L) for 28 days. The results revealed that MPs were accumulated on the chorion and ingested by larvae from 2 days post-hatching. High levels of MPs (20 and 200 μg/L) decreased the hatchability, delayed the hatching time, and suppressed the growth, whereas Phe inhibited hatching and caused malformations in larvae. The presence of MPs at 20 and 200 μg/L did not alter the toxicity of Phe. By contrast, combined exposure to 2 μg/L MPs and Phe increased the hatchability by 25.8%, decreased malformation and mortality rates, and restored Phe-induced abnormal expressions of cardiac development-related genes. The reduced early developmental toxicity could be attributed to the decreased bioavailability and bioaccumulation of Phe by the low level of MPs. These findings contradicted the view that MPs would aggravate the toxicity of organic pollutants, and future studies are warranted to elucidate the ecological risks of marine MPs.