Environmental Protection Areas (EPA) are of extreme importance for species conservation and establishment. We investigated different areas of riparian forests in the Environmental Protection Area of Ibirapuitã, southern Brazil. We analyzed the environmental quality of these areas by studying the lichen community and using the index of atmospheric purity (IAP) with the environmental classification factor (ECF) as the correction factor. The lichen community was analyzed in 12 riparian forest stands located in the southern region of EPA. Lichens were registered on 60 tree barks, from 50 cm to 150 cm above the ground, on both north and south sides. A cluster analysis was used to test whether there were changes in lichen species similarity among communities from each forest vegetation stands. A total of 193 lichen species were registered. The stands were classified into poor-lichen, transition zone, and normal for lichen development. The cluster analysis showed distinct groups, demonstrating differences in species composition among the stands. Indicator lichen species were registered in 80 % of the studied stands. In the most conserved areas, higher species richness and a greater number of fruticose species were registered, besides the presence of key species such as the genus Lobaria. The conservation of forest areas in environmental protection areas is essential for biodiversity conservation. Our results confirm the usage of the index of atmospheric purity with ECF to evaluate environmental quality of forest areas.