This study presents the first record of Halodule pinifolia on the eastern coast of Sri Lanka, approximately 310 km along the coastline from the previously recorded location (Kapparathota, Weligama). Further, this study describes the new locality of the nationally endangered seagrassspecies Halophila beccarii to Valaichchenai Lagoon, 26.5 km north of Batticaloa Lagoon, where itwas previously recorded, along with the presence of two other species, Halophila ovalis and Haloduleuninervis. While the species composition the seagrass habitat of Valaichchenai Lagoon might changein the near future due to the impact of climate change, multiple threats already exist at these newlydiscovered seagrass habitats, including multiday fishing vessel movements, the collection of shellson the seagrass beds, and solid waste dumping into the lagoon. Decline of seagrass abundance inValaichchenai Lagoon would negatively impact the food security and income generation of fishers.Therefore, a well-established legislative framework and systematic long-term monitoring of seagrassin Valaichchenai Lagoon are essential in order to develop seagrass conservation plans beforepopulations decline significantly or become locally extinct.