The main objective of this study was to evaluate the influence of vegetated beds on macrofauna community structure of the estuarine soft bottoms of the Patos Lagoon, southern Brazil. Comparative analyses were made by faunal samples collected inside and outside in two kinds of vegetated beds: a sea grass meadows during the summer period and, an algal mats at winter one. The presence of theses vegetated beds had essentially favoring highest densities of epifaunal organisms by increase of substratum for fixation and feeding, which could to result at decrease of evenness and, consequently, of the diversity of macrofauna inside these beds such as registered at summer survey. Differences in the both evenness and diversity at winter survey as well in the composition and number of species at both times were not observed among habitats. These results indicate that the increase at structural complexity of habitat promoted by presence of vegetated beds not necessarily favoring the increase of the macrofauna diversity of the estuarine region of the Patos Lagoon.