The growing population is putting increasing pressure on marine ecosystems due to the exploitation of species for human consumption. Marine protected areas are being put in place to safeguard marine ecosystems, but recent studies have questioned if this is the most effective approach, or whether effects from intense land use are undermining these protection measures. One ecosystem under threat from overexploitation is seagrass beds. I conducted a field survey, using belt-transect and quadrat sampling methods in order to investigate the direct and indirect effect of marine protection and land use intensity on seagrass coverage and the characteristics of macroinvertebrate communities in the seagrass beds around Zanzibar in 2023. I found that marine protection significantly affects seagrass coverage, as well as the abundance, diversity, and composition of invertebrates. Marine protection reduced the abundance of invertebrates, mainly by lowering the number of urchin-barren forming Echinometra mathaei urchins that were dominating the seagrass beds. I also found higher diversity in protected areas, as there was less resource domination by urchins, allowing more species to coexist. This lower diversity in fished areas was also due to the selective removal of species by humans, which directly lowers the number of species present and indirectly damages species interactions, allowing fewer species to coexist in an area. Additionally, I found that land use intensity substantially affects invertebrate composition. At higher land-use intensity the composition of invertebrates was largely made up of Echinoderms and Molluscs. Some echinoderms are known to increase greatly in numbers in areas with anthropogenic pollutants in the water, and molluscs are one of the groups most resistant to the effects of increased sedimentation, indicating that anthropogenic stressors are severely influencing community composition. I found lower seagrass coverage in marine-protected areas; however further study is needed to fully understand this relationship. This study emphasises that marine protected areas play a crucial role in safeguarding seagrass ecosystems, but also that the impact of land use intensity should not be disregarded, and should be included as a critical factor when designating new marine protected areas.