Here we present Oligonucleotide Retrieving for Molecular Applications (ORMA), a series of integrated scripts in Matlab, which performs an accurate search of all the positions able to specifically discriminate one species among homologous ones, based on the 16S rRNA gene sequence. ORMA also performs an accurate selection of high-quality oligonucleotide probes to be used in molecular applications. Automated and computerbased methods can be very useful for performing accurately and rapidly all the requested operations, through the many steps between the original, complete, set of sequences and the final list of application-oriented probes.