The phototrophic flagellate flora of the Barra Lagoon (22°57′ S and 42°47′ W), Rio de Janeiro State, southeastern Brazil, is described. The lagoon is a shallow, oligohaline, hypertrophic ecosystem in which Cyanophyceae, Chlorophyceae and phytoflagellates are dominant. Between October 1990 and August 1993, weekly integrated samples were collected from a bay, using a plexiglass tube, 8 cm diameter and 1m length. All identifications, descriptions and measurements were carried out on live or in Lugol-fixed material. A total of 30 taxa, belonging to Euglenophyceae (5), Cryptophyceae (7), Raphidophyceae (1), Dinophyceae (4), Chrysophyceae (3), Prymnesiophyceae (2), Prasinophyceae (7) and Chlorophyceae (1) were identified. All the phytoflagellate species identified have been recorded previously from temperate sites. Nine of them were registered in a tropical water for the first time, suggesting that they have much broader distributions. Gymnodinium sanguineum, Pavlova lutheri and Pyramimonas grossii were the most frequently observed phytoflagellates in this study. The seasonal occurrence and some environmental requirements of selected phytoflagellates species are discussed.