Microplastics (MPs) are ubiquitous in marine environment. The prevalence of MPs in coastal and lagoon sediments, and water were studied in two Marine Protected Areas (MPAs); Bundala National Park (BNP) and Hikkaduwa Marine National Park (HNP) in Sri Lanka. Both areas are important for turtles, birds and coral ecosystems, all of which are particularly threatened by MPs. Abundance of MPs was generally higher in both coastal sediments and waters in HNP (111±29 MPs/m² for sediments and 0.515±0.054 MPs/m³ for water) than in the BNP (102±16 MPs/m² for sediments and 0.276±0.077 MPs/m³ for water). The most common shape and polymer type of MPs were fragments and Polyethylene respectively. This research is the first to survey MPs in MPAs in Sri Lanka and provides a baseline of MPs pollution in these environments for future research and management.