Abstract The growth and reproduction of the marine seagrass foundation species Zostera marina (eelgrass) are threatened by rising sea surface temperatures (SSTs). After both natural and anthropogenic disturbances, the recovery of Z. marina largely depends on seed germination and seedling establishment. Therefore, understanding the effects of increasing water temperature on the phenology and intensity of flowering is critical for predicting the persistence of Z. marina and its associated ecosystems. The effects of increasing SST on Z. marina flowering were investigated using long-term records (2002–2018) of Z. marina flowering and daily SSTs along the southern coast of Korea. Significant SST increases occurred during the study period. The annual maximum SST increased at a faster rate than the annual mean SST, whereas no warming trend was observed for the minimum winter temperature. Gradual declines in the reproductive intensity of Z. marina were observed during 2011–2018, when annual mean SST increased rapidly and summer marine heatwave (MHW) events became more intense and frequent. Reproductive parameters such as flowering shoot density, flowering frequency, and reproductive allocation showed significant negative relationships with mean SSTs. Thus, increasing heat stress due to sea warming would have led to decreased reproductive output of Z. marina over the study period. The results of this study suggest that warmer water temperature in the future may decrease the reproductive performance of Z. marina and limit this species’ capacity for recovery via seedling recruitment. Measuring long-term sexual reproduction in Z. marina may be useful as a bioindicator of sea warming and will improve our understanding of seagrass responses to climate change.