Borneo is one of the regions expected to have the highest diversity of seagrasses in the world. However, the diversity of seagrasses has scarcely been studied in Brunei Darussalam. The diversity of seagrasses at the intertidal and subtidal zones in Brunei was extensively surveyed in 2016. Six species of seagrasses were found at Pulau Muara Besar and Pulau Bedukang, and this was the first time that three of them (Halophila beccarii, Halodule pinifolia, and Cymodocea rotundata) had been recorded in Brunei. The total area of seagrass distribution around the two islands was approximately 1.5 km2. The present study extends the distribution of seagrasses on Borneo and suggests that Brunei has a rich seagrass diversity and an aquatic ecosystem supported by the seagrasses.