Florigen and antiflorigen genes within the phosphatidylethanolamine-binding protein (PEBP) family regulate flowering in angiosperms. In eelgrass (Zostera marina), an estuarine foundation species, flowering, and seed production are crucial for population resilience. Yet, the molecular mechanism underpinning flowering remains unknown. Among 13 PEBP genes in Z. marina (ZmaPEBP), we showed that four genes (ZmaFT2, ZmaFT4, ZmaFT9, and ZmaTFL1a) altered flowering time when overexpressed in Arabidopsis. We analyzed gene expression in different tissues and throughout the growth season from perennial and annual populations in Willapa Bay and Yaquina Bay, USA. Across six sites exhibiting different degrees of population genetic structure, ZmaFT2 and ZmaFT4 were expressed in leaves of vegetative and reproductive shoots and in rhizomes of reproductive shoots. ZmaFT9 was solely expressed in leaves of vegetative shoots, while ZmaTFL1a levels increased after flowering shoots developed. Our results suggest that ZmaFT2 and ZmaFT4 may promote flowering, while ZmaFT9 may inhibit flowering in eelgrass.