This study evaluated the variation of tree species composition of 35 wetland forest areas in Southeast and South Brazil. The analysis of the floristic composition was based on a floristic checklist containing 602 species of 23 alluvial forests (seasonally inundated) and 12 swamp forests (permanently waterlogged). The species were classified, using a χ2 test, according to the habitat preference in: 1) swamp forest species, e.g. Magnolia ovata (A. St.-Hil.) Spreng., Dendropanax cuneatus (DC.) Decne & Planch. and Calophyllum brasiliense Cambess.; 2) alluvial forest species, e.g. Sebastiania commersoniana (Baill.) L.B. Sm. & Downs, Ocotea pulchella Mart. and Sorocea bonplandii (Baill.) W. Burger et al. and 3) non preferential species, e.g. Luehea divaricata Mart. & Zucc., Syagrus romanzoffiana (Cham.) Glassman and Copaifera langsdorffii Desf. Multivariate gradient analysis (Detrended Correspondence Analysis) showed higher clustering of swamp forest areas than aluvial forest areas, indicating close florist similarity in the first group. The results indicated that the environmental heterogeneity associated to different flood regimes is determinant in defining the phytogeographic patterns of wetland forest areas.