Biodiversity assessments within seagrass beds were conducted in six sites in Lamu, Kenya; namely, Kiweni, Tauzi, Wange, Ntopate, Manda toto and Ngoi. The objective of the assessment was to collect baseline information of the seagrasses of Lamu County in Kenya. Our findings revealed that nine out of the twelve seagrass species found in Kenya were found in the study sites. The dominant seagrass species Thalassodendron ciliatum was found to occur in deeper subtidal areas, while the pioneering species occurred in intertidal shallower areas. Average shoot densities per site ranged from 2.4 ± 1.7 shoots m^-2 of Cymodocea serrulata to 1025.9 ± 139.3 shoots m^-2 of Syringodium isoetifolium in Ngoi. Canopy heights ranged from 0.1 ± 0.1 cm of Halodule ovalis in Tauzi to 16.3±1.3.5 cm of Syringodium isoetifolium in Ngoi. Although the seagrass species characteristics were much lower than that found in similar mangrove fringed seagrass beds of Gazi Bay, the majority of the fish found in these seagrass areas were invertivores which indicates that these seagrass sites form a refugia for adult fish populations with nursery grounds being located elsewhere.

This study forms the first comprehensive assessment of the seagrasses of Lamu and it provides important baseline information on seagrass beds. Such biodiversity information provides important support for decision-making for coastal areas that are targeted for infrastructural development such as Lamu. Biodiversity information of such critical habitats form a critical data base for marine spatial planning and can be used to effectively guide the integration of biodiversity and coastal livelihoods in the sustainable development of Kenya's coastal areas.