The distribution of fatty acids in 13 species of macroalgae (Chlorophyta, Ochrophyta and Rhodophyta) and 1 seagrass (Spartina sp), collected on the Rio de Janeiro state coast was determined. The results were evaluated in search of correlations between the taxonomic and phylogenetic position of these macrophytes. Statistical analyses showed the effectiveness as taxonomic and phylogenetic markers of the distribution of the methyl fatty acid esters in these macrophytes.