Environmental quality indicators based on biological community indexes have been largely used in environmental characterization and monitoring programs. New community indexes have been proposed in order to refine such applications. In this work, we used the habitat specificity index to assess the specificity of the species and genera of Chlorococcales related to habitat, and the contribution of the relative habitat specificity, at the landscape scale. Thus, we conducted a survey in 5 sample sites in the medium stretch of the Itajaí-Mirim River, between the counties of Brusque e Botuverá, in order to investigated the patterns of phytoplankton Chlorococcales, in the summer season. It was identified 31 species belonging to 12 genera. The highest habitat specificity was found in the sample site located in Botuverá County (pristine), whereas the lowest, in the Brusque County (disturbed). At such scale, the generic specificity index showed clearly groups of habitat specificity.