This study aimed at comparing phytoplankton taxonomic classes and morpho-functional attributes in two shallow tropical reservoirs with different nutrient levels and representing extremes of the alternative stable states theory. The reservoirs, locally called Ninféias Pond (23°38′18. 95″S; 46°37′16.3″W) and Garças Pond (23°38′40.6″S; 46°37′28.0″W), are located in the city of São Paulo, southeastern Brazil. Ninféias Pond is oligo-mesotrophic and has abundant submerged macrophytes; Garças Pond is eutrophic without submerged macrophytes, with cyclic cyanobacterial blooms. Sampling was carried out monthly from January to December 1997. Phytoplankton species were classified according to taxonomic classes and the following criteria: life form, size, biovolume, life strategy (C-S-R) and functional group. Statistical differences in taxa contribution were reported for both lakes considering all criteria tested, especially life forms. Taxonomic classes dominating Ninféias Pond were Prymnesiophyceae and Dinophyceae, which strongly influenced a community characterized by nanoplanktonic unicellular flagellated C/S-strategists, and the main functional groups were X2, L O and W1. Garças Pond phytoplankton community was dominated by species belonging to Cyanobacteria and colonial non-flagellated nano/micro-planktonic S-strategists, and the main functional groups were M, SN and LM. Differences in trophic status are probably the main factor triggering such differences. However, the presence of macrophytes in Ninféias Pond also seems to qualitatively influence its phytoplankton community, favoring flagellated species.