Knowledge of seagrass distribution is limited to a few well-studied sites and poor where resources are scant (e.g. Africa), hence global estimates of seagrass carbon storage are inaccurate. Here, we analysed freely available Sentinel-2 and Landsat imagery to quantify contemporary coverage and change in seagrass between 1986 and 2016 on Kenya's coast. Using field surveys and independent estimates of historical seagrass, we estimate total cover of Kenya's seagrass to be 317.1 ± 27.2 km2, following losses of 0.85% yr−1 since 1986. Losses increased from 0.29% yr−1 in 2000 to 1.59% yr−1 in 2016, releasing up to 2.17 Tg carbon since 1986. Anecdotal evidence suggests fishing pressure is an important cause of loss and is likely to intensify in the near future. If these results are representative for Africa, global estimates of seagrass extent and loss need reconsidering.