Seagrasses provide diverse ecosystem services that support communities, yet, they are among the most threatened marine habitats. Efforts to conserve and sustainably manage seagrasses are increasing, particularly amidst the era of climate change, in which they play a critical role. However, these activities often received less attention or were slow in gaining momentum partly due to a lack of societal recognition of seagrasses and their importance. Thus, in this study, we collected community perceptions of seagrass ecosystem services and threats from 391 respondents in Karimunjawa National Park (KNP), a nationally declared protected area in Indonesia. We aim to provide insights on people’s recognition of seagrasses from a local scale with strict protection measures. Overall, respondents showed varying perceptions of seagrass ecosystem services, with provisioning services more highly perceived than regulating services. The perceived level of threats was inconclusive, though, reclamation along shorelines received higher rates (leaning toward most damaging) than other threats such as natural disasters and illegal fishing activities. Sociodemographic attributes of respondents were found to influence their perceptions, with occupation as the most pronounced driving factor. The variations observed in seagrass perceptions suggest that there is a need to strengthen and/or enhance seagrass awareness and education campaigns, which is in line with the increasing demand that public perceptions matter for the conservation and sustainable management of seagrass ecosystems. We presented here the use and insights of community perceptions for seagrass blue carbon conservation in KNP, and consequently in Indonesia, where seagrass meadows are considered globally important carbon sinks.