The phytoplankton composition and abundance in the large, subtropical coastal Merin Lagoon (Brazil-Uruguay) were analyzed seasonally between 1998 and 1999, based on plankton net and bottle samples in 38 stations. The lagoon is connected to the choked Patos Lagoon forming a complex ecosystem with a drainage basin of 201626 km2. Temperature and conductivity presented similar seasonal trends, with lower values (mean 15 °C and 70 µS cm–1, respectively) in austral winter (July–August 1998) and higher (mean 25 °C and 105 µS cm–1, respectively) in summer (January 1999).Atotal of one hundred and fifty three microalgae belonging to 8 classes were identified in the lagoon. Most species belong to the genera Staurastrum (8 species). and Scenedesmus (6 species). The species of genera such as Aulacoseira (Bacillariophyceae), Cryptomonas (Cryptophyceae), Monoraphidium (Chlorophyceae) and Planktolyngbya (Cyanobacteria) were present throughout the year. Diatoms predominated in spring and shared dominance with Cyanobacteria in summer and autumn. In winter, Chlorophyceae and Cryptophyceae dominated in the community. Phytoplankton spatial variability and abundance reached their maximum in March’98 (autumn) with 3600 ind mL–1, while in November (spring) relatively low abundances were found in the lagoon (average 1126 cells mL–1). The abundant phytoplankters were Planktolyngbya limnetica (943 cells mL–1), Aulacoseira (1874 cells mL–1), Staurosira construens (847 cells mL–1) and an unidentified unicellular volvocalean (1066 cells mL–1).