Sundarbans, the world's largest mangrove ecosystem, is unique and biologically diverse. A study was undertaken to track temporal succession of phytoplankton assemblages at the generic level (≥10？μm) encompassing 31 weeks of sampling (June 2010–May 2011) in Sundarbans based on microscopy and hydrological measurements. As part of this study, amplification and sequencing of type ID rbcL subunit of RuBisCO enzyme were also applied to infer chromophytic algal groups (≤10？μm size) from one of the study points. We report the presence of 43 genera of Bacillariophyta, in addition to other phytoplankton groups, based on microscopy. Phytoplankton cell abundance, which was highest in winter and spring, ranged between 300 and 27,500？cells/L during this study. Cell biovolume varied between winter of 2010 (90–35281.04？μm3) and spring-summer of 2011 (52–33962.24？μm3). Winter supported large chain forming diatoms, while spring supported small sized diatoms, followed by other algal groups in summer. The clone library approach showed dominance of Bacillariophyta-like sequences, in addition to Cryptophyta-, Haptophyta-, Pelagophyta-, and Eustigmatophyta-like sequences which were detected for the first time highlighting their importance in mangrove ecosystem. This study clearly shows that a combination of microscopy and molecular tools can improve understanding of phytoplankton assemblages in mangrove environments. 1. Introduction The most implicit elements of the global carbon cycle are those involving the coastal environments that embrace a great variety of habitats including mangroves which are located in tropical and subtropical regions of the world. These ecosystems are known to account for 14–30% of the marine primary production [1] and annual sequestration of approximately 22.8 million metric tons of carbon [2]. Phytoplankton forms the basis of the aquatic primary production in mangrove environments. These photosynthetic organisms are major contributors of high fish productivity in mangrove habitats [3]. Approximately 41% of the world’s mangrove occurs in South and Southeast Asia, out of which Indonesia alone accounts for 23% [4]. Sundarbans (21°32′ and 22°40′？N; 88°05′ and 89°E), world’s largest contiguous deltaic mangrove ecosystem located at the apex of Bay of Bengal, encompasses over 102 islands with a network of innumerable rivers, rivulets, and creeks. This vast deltaic region is formed at the estuarine phase of the Ganges-Brahmaputra and Meghna river system across India and Bangladesh covering a total area of approximately 10,000？km2 and tidally influenced by
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