Brazilian Atlantic Forest is one of the 25 biodiversity hot-spots in the world. Part of this forest, which is located in Paraná state, is considered the most conserved in Brazil with 100% of its area protected by laws. Much is known about the diversity of its fauna and flora, but little it is known about its microbial diversity. This work represents the first soil microbe diversity description of the Atlantic forest using culture-independent molecular approach. Ten samples of soils, named MA01 to MA10, were collected along the Graciosa Road that crosses the conserved portion of the forest. Total DNA of these samples were extracted and used as templates in a PCR reaction using 16S rRNA universal primers for Bacteria and Archaea. The PCR amplification products were cloned into pGEM-T vector and the diversity of 16S rRNAs was determined through the partial sequencing. DNA sequences comparison of the 754 clones sequences with the RDP II database of 16S rRNA indicated predominance of phylum Acidobacteria in the soil samples with 45,9%. The second more representative phylum found was of the Proteobacteria with 26% of the sequences. Representatives of thermophilic bacteria phylum Thermomicrobia and Thermotogae, and candidates phylum OP10, also thermophilics, and SPAM were also found. Moreover, 17% of the sequences could not be grouped with sequences of 16S rRNA of known bacteria, therefore, they were not classified. The 16S rRNA gene sequencing also allowed the identification of bacteria with potential application in biotechnology. The Shannon-Weaver diversity index was calculated for the ten soil samples individually reaching a maximum of 4,12 in MA02 sample and a minimum of 3,57 in MA08 sample. The MA01 sample had the highest diversity, where 77 sequences were distributed in 67 species (95% of similarity between sequences). No Archaeal representant were found in the tested samples.