We investigated the sediment carbon (C) stocks, sequestration and sources in tidal flats and their adjacent mangroves in two coastal wetlands in Hong Kong (the Mai Po Nature Reserve (MPNR) and Ting Kok (TK)), part of a megacity of ∼20 million. At both locations, the C stock of tidal flats was lower than that of mangroves. In MPNR, tidal flats indicated a higher C burial rate (75.2 g C m−2 yr−1) compared to mangroves (64.3 g C m−2 yr−1). The C of tidal flats mainly originated from mangroves and riverine sources, while those in deeper sediments (below 60 cm) in the mangroves originated from the tidal flats. In TK, the C of tidal flats was dominated by oceanic sources. Our study indicates that tidal flats are also important in coastal C sequestration. On highly urbanized coasts, tidal flats and their connected mangroves can play a critical role for C mitigation.