Microplastic pollution has recently been identified as a major issue for the health of ecosystems. Microplastics have typically sizes of less than 5 mm and occur in various forms, such as pellets, fibres, fragments, films, and granules. Mangroves and coral reefs are sensitive and restricted ecosystems that provide free ecological services such as coastal protection, maintaining natural cycles, hotspots of biodiversity and economically valuable goods. However, urbanization and industrial activities have started contaminating even these preserved ecosystems. Here we review sources, occurrence, and toxicity of microplastics in the trophic levels of mangrove and coral reef ecosystems. We present detection methods, such as microscopic identification and spectroscopy. We discuss mitigating measures that prevent the entry of microplastics into the marine environment.