The extensive presence of microplastics (MPs) in marine ecosystems constitutes a major threat to aquatic environments. The gametes of the marine invertebrate Mytilus galloprovincialis, which is essential for coastal ecosystems, are released directly into the water, potentially exposing them to environmental microplastics (EMPs). This study examined the effects of exposing M. galloprovincialis gametes to 50 or 100 µg/L EMP for 1 h on fertilization rates, larval quality, and the molecular mechanisms underlying the induction of apoptosis and shell growth. Our findings show that increased EMP concentrations correlate with reduced fertilization success and higher rates of larval malformations, indicating negative impacts on embryonic development. Additionally, DNA degradation in larvae is related to the EMP concentration. The apoptosis-associated proteins Bax, P53, and Cas-3 are upregulated, whereas Bcl-2 and DNA-ligase are downregulated with increasing EMP concentrations. Prothymosin-ɑ (PTMA), which is crucial for cell proliferation, also decreases with increasing EMP concentrations, contributing to impaired cell proliferation and growth imbalances. Reduced HRG gene expression is correlated with decreased shell growth and larval malformations. This study underscores the detrimental impact of EMPs on bivalve gametes, which impacts fertilization success and larval quality and highlights the potential risks to species survival and marine ecosystem stability.