Seagrass beds occur globally in both intertidal and subtidal zones within shallow marine environments, such as bays and estuaries. These important ecosystems support fisheries production, attenuate strong wave energies, support human livelihoods and sequester large amounts of CO₂ that may help mitigate the effects of climate change. At present, there is increased global interest in understanding how these ecosystems could help alleviate the challenges likely to face humanity and the environment into the future. Unlike other blue carbon ecosystems, i.e., mangroves and saltmarshes, seagrasses are less understood, especially regarding their contribution to the carbon dynamics. This is particularly true in regions with less attention and limited resources. Paucity of information is even more relevant for the subtidal meadows that are less accessible. In Kenya, much of the available information on seagrasses comes from Gazi Bay, where the focus has been on the extensive intertidal meadows. As is the case with other regions, there remains a paucity of information on subtidal meadows. This limits our understanding of the overall contribution of seagrasses in carbon capture and storage. This study provides the first assessment of the species composition and variation in carbon storage capacity of subtidal seagrass meadows within Gazi Bay. Nine seagrass species, comprising of Cymodocea rotundata, Cymodocea serrulata, Enhalus acoroides, Halodule uninervis, Halophila ovalis, Halophila stipulacea, Syringodium isoetifolium, Thalassia hemprichii, and Thalassodendron ciliatum, were found. Organic carbon stocks varied between species and pools, with the mean below ground vegetation carbon (bgc) stocks (5.1 ± 0.7 Mg C ha⁻¹) being more than three times greater than above ground carbon (agc) stocks (0.5 ± 0.1 Mg C ha⁻¹). Mean sediment organic carbon stock (sed C_org) of the subtidal seagrass beds was 113 ± 8 Mg C ha⁻¹. Combining this new knowledge with existing data from the intertidal and mangrove fringed areas, we estimate the total seagrass ecosystem organic carbon stocks in the bay to be 196,721 Mg C, with the intertidal seagrasses storing about 119,790 Mg C (61%), followed by the subtidal seagrasses 55,742 Mg C (28%) and seagrasses in the mangrove fringed creeks storing 21,189 Mg C (11%). These findings are important in highlighting the need to protect subtidal seagrass meadows and for building a national and global data base on seagrass contribution to global carbon dynamics.