Monthly sampling in mangrove intertidal sediments of Andaman Archipelago was carried out during a 1-year study (January to December, 2013) in order to analyse the spatial and temporal distribution of microphytobenthos (MPB) and MPB biomass (sediment chlorophyll-a (chl-a)) in the surficial layer 0-1 cm. The MPB community was mainly composed of diatoms. The MPB biomass concentration in surface sediment (0-1 cm) ranged from 0.7 to 16.98 μg cm. Population density of benthic diatoms varied from 78 to 224 ind cm. This study identified 41 diatom taxa (27 pennate diatoms, 14 centric diatoms) in the sediment, and among all the diatom taxa, we distinguished few true planktonic species-Coscinodiscus centralis, Coscinodiscus marginatus, Leptocylindricus danicus, Planktoniella sol, Thalassiosira decipiens, Thalassionema nitzschioides and Thalassiothrix longissima. Overall, a high percentage of diatoms were pennate (81%) as opposed to centric. Based on benthic diatom abundance, species composition and distribution, MPB assemblages of sampling stations were grouped into two distinct clusters: one with St. 1 and St. 3 and another one with St. 2 and St. 4. Canonical correspondence analysis (CCA) revealed seasonality as the most important factor determining variability in diatom species composition among sampling sites. There was a distinct seasonal pattern in MPB biomass distribution and benthic diatom cell density during monsoon and post-monsoon seasons. Our results suggest that among various physical and chemical variables studied, greater levels of overlying water nutrients and sediment textures significantly correlated and were conducive factors for MPB. This is the first detailed study on the MPB from these mangrove sediments, providing benchmark data for future studies about these remote groups of Andaman and Nicobar Islands.