This work aimed to evaluate the influence of salinity and flooding frequency on distribution and biomass of seaweed communities occurring on trunks and roots of mangrove trees in Babitonga Bay, SC (26º15’S, 48º35’W). The seaweeds were collected in tree slices with 10 cm height from the bottom to its upper limit on the trees, in oligohaline, mesohaline e euhalinde areas of the bay. The seaweeds were sorted by species, dried until constant weight, and presented as algae biomass per trunk area (g dm (dry mass) m-2 of substrate). Cluster analysis was applied to study these communities, using biomass of each species in each flooding level, in each site of the bay. The average biomass in euhaline place (195,9 ± 58,8 g dm m-2) was significantly higher than in oligohaline place (36,9 ± 13,5 g dm m-2). There was no significant difference in biomass from mesohaline to euhaline, neither from mesohaline to oligohaline, but a positive correlation occurred between biomass and salinity (r2=0,83). In the cluster analysis the groups formed were: 1) euhaline site with flooding frequency higher than 92% of time, dominated by Bostrychia montagnei; 2) euhaline site with flooding frequency lower than 92% of time, dominated by Bostrychia tenella; 3) mesohaline site, dominated by Bostrychia calliptera and Bostrychia pinnata; 4) oligohaline site, dominated by Catenella caespitosa. The mesohaline group, as much as the oligohaline group was spitted in smaller groups with flooding frequencies lower or higher than 92% of time. Differences were also observed in diversity, and number of species was higher in euhaline site (15 species) and lower in olighaline site (4 species). The results of this works show how important salinity and flooding frequency are to structure of mangrove seaweeds in Babitonga Bay.