The growth in knowledge about Protura, after their relative recent discovery (SILVESTRI, 1907), remained rather limited. Due to their small body size, and to their cryptic lifestyle in the soil, only few specialists are able to determine these insects to species level. Traditional identification is based on a combination of chaetotaxy, porotaxy, and morphometrics. The need to clear specimens before identification by using lactic acid, imposed an obstacle for the inclusion of a molecular-genetic approach in studies of Protura: no one is able to identify species before clearing specimens thereby destroying the DNA, and vice versa nobody was able to analyze DNA without destroying the specimens. The recent implementation of a non-destructive method (BÖHM et al., 2011) which enables the extraction of whole genomic DNA without destroying the cuticular exoskeleton, thus provides an unexpected opportunity to modernize proturan systematics. A first study using the DNA barcoding region of the mitochondrial CO1 gene, and a fragment of the nuclear 28S rDNA gene revealed a perfect match of molecular results with morphological identification, however, with unexpected high variation among different populations of the same species (RESCH et al., 2014). This presentation gives an overview of the problems and limitations of the traditional morphological methods and the first results of our integrative approach.