Seagrass meadows provide diverse ecosystem services that directly or indirectly benefit the coastal communities. Despite this, they are among the most threatened coastal ecosystems. Though coastal and marine conservation actions have progressed over the years, seagrasses received less attention compared with other more charismatic ecosystems such as coral reefs and mangroves. Among the influencing factors, the lack of societal recognition of what seagrasses are and their importance underlies the global crisis of seagrass conservation. Thus, in this study, we gathered rural and urban perceptions of seagrass ecosystem services, their threats, and management-related activities at the unit of barangay or village in the Philippines. Overall, rural respondents displayed higher awareness of seagrass ecosystem services than urban respondents. Socio-economic status and personal connection or direct experience to these services influenced their perceptions. Local-level threats were also perceived and recognizing these at the early onset can avoid severe habitat degradation. Though the role of seagrass blue carbon in climate change mitigation was barely discussed in local contexts, the impact of climate change-induced stressors on seagrass was perceived by the respondents. Thus, local stakeholders, practitioners, and policymakers have the opportunity to design future seagrass-focused management plans and programs in the era of climate change.