Wetlands of southern Brazil exhibit unique habitat attributes, such as climate pattern and vegetation cover, that can function as an environmental filter for the establishment of species of Neotropical anurans and influence the composition of anuran assemblages. We examined the role of habitat heterogeneity in the composition and relative abundance of anuran species in subtemperate wetlands of southernmost Brazil. We carried out standardized sampling between May 2009 and April 2011 to examine anuran assemblages in marshes associated with grasslands and coastal dunes, as well as habitat heterogeneity. Habitat heterogeneity and anuran species richness were higher in grasslands. Abundance and species dominance, on the other hand, were higher in dunes. This might be due to more restrictive abiotic filters in dunes, such as the low heterogeneity of vegetation cover and lower availability of water bodies. The most common species in grasslands, Leptodactylus cf. latrans, Elachistocleis bicolor, and Pseudis minuta, exhibited a stronger association with habitats with larger and deeper water bodies and with the presence of floating vegetation. The most abundant species found in dunes, Rhinellla arenarum, Odontophrynus maisuma, and Physalaemus biligonigerus, had a stronger association with low vegetation. In addition to habitat associations, the ability to bury themselves might be a behavioral adaptation to dunes that favor species such as O. maisuma and P. biligonigerus, even under extreme microclimatic conditions. Our findings support the importance of the configuration of vegetation cover as well the heterogeneity of water bodies for the establishment of anuran species in subtemperate marshes of southern Brazil.