This study aimed to identify taxa belonging to the genera Monoraphidium and Ankistrodesmus (Chlorophyceae, Chlorophyta) in two wetland areas of Pantanal dos Marimbus (Baiano and Remanso) in the Marimbus-Iraquara Environmental Protection Area, Bahia State, Brazil, and contribute to the knowledge of Chlorophyceae of Bahia State and Brazil. The materials studied, which were of periphytic and metaphytic origin, came from 64 samples collected in April and June 2011. We identified 18 taxa, 13 from Monoraphidium and five from Ankistrodesmus. Eight taxa were additions to the continental microalgae flora of Northeastern Brazil. Two taxa rarely found in Brazil were collected during the study: Monoraphidium dybowskii and M. litorale.