Being a primary producer, Microphytobenthos (MPB) play an important role in the benthic ecosystem of mangrove swamps. The temporal and vertical distribution of MPB biomass, expressed as chlorophyll a (Chl a), was investigated in mangrove swamps on the Qi’ao island and the Futian Mangrove Nature Reserve, Guangdong Province, South China. Both locations are situated in the Zhujiang (Pearl River) Estuary. For each location, bi-monthly sampling was carried out at four sites during low tide period. Except one site on the Qi’ao Island, which was in Phragmites australis marsh, all sites were in mangrove swamps. The Chl a concentration in surface (0–1 cm) sediment ranged from 0.2 µg/cm3 to 8.3 µg/cm3 in the Qi’ao Island and from 2.1 µg/cm3 to 15.6 µg/cm3 in the Futian Mangrove Reserve. The peak Chl a concentration occurred in winter or early spring, while the lowest Chl a concentration, with a value of about one quarter of the peak, was observed in summer or early autumn. The vertical distribution of Chl a concentration exhibited an exponential decline with depth, which indicated a muddy sediment with high organic matter, and the slope of the curve was positively related to Chl a concentration in the surface sediment. The MPB biomass of the Qi’ao Island was significantly lower than that of the Futian Mangrove Reserve. Our results suggest that the overlaying water quality might influence the MPB biomass in surface sediments.