Seagrass meadows, one of the world′s greatest natural assets, are globally declining due to direct-anthropogenic (e.g., pollution, coastal development, run-off) and climate change (e.g., cyclones, floods, marine heatwaves) threats. One of the primary constraints in seagrass management and restoration is a lack of societal awareness about their role in the marine environment, their importance to human well-being, and their vulnerability. Public perception studies are useful tools to assess communities′ ecological knowledge and attitudes. The Great Barrier Reef World Heritage Area (GBRWHA), famous worldwide for its iconic coral reef, also hosts one of the world′s largest areas of seagrass meadows, which provide many ecosystem services to the associated communities (e.g., nursery habitat, coastal protection, carbon sequestration etc.). However, the perception of seagrasses among coastal communities of the GBRWHA is poorly understood. Through an online survey of marine recreational users, we assessed public awareness of the role seagrasses play, its benefits, and threats to seagrasses in the GBRWHA, in comparison to coral reefs. Our results showed that there is an imbalance in perception of the role and ecosystem services provided by seagrasses and coral reefs among frequent visitors of the GBRWHA. Only 17% of respondents recognized ‘seagrass’ as a habitat of the GBRWHA. Ecosystem services from coral reefs were considered greater than from seagrasses (p < 0.05). Compared to previous studies, a higher percentage of participants believe in climate change (75%). Nevertheless, the general perception is that climate change impact magnitude is higher in coral reefs compared to seagrasses (p < 0.05). Additionally, climate change mitigation, a seagrass-related ecosystem service, was equally attributed to coral reefs and seagrasses (p > 0.05). Willingness-to-pay for coral reef restoration was higher than for seagrass (p < 0.05). For both marine habitats, willingness-to-pay for restoration was higher in younger people and participants with a university degree. Content analysis showed that people believe that marine habitats′ conservation/restoration can be achieved as a collective effort. On the other hand, a lack of trust in government actions was identified as a barrier to willingness-to-pay. These results confirm the need to raise awareness about the importance of seagrasses and of its vulnerability to climate change. To achieve that, we provide two key recommendations: to enhance purposeful experiences through citizen science and to increase effective scientific communication.