The problem of designing specific oligonucleotide probes for the identification of target species has already been addressed by a certain number of software (13) (14) (15) (16) . At present, there is no preferential reference strategy for designing microarrays for species identification based on 16S rRNA sequences: many authors rely on academic software (17, 18) , others develop their own scripts (19, 20) . Among the currently available academic software, ARB (21) and PRIMROSE (22) are very diffused, both being tools implemented specifically on 16S rRNA, structured for interacting with and retrieving sequences from specific databases and operating a probe design on the basis of the phylogenesis of the species under analysis. Also, some commercial software, like Oligo 7 (Molecular Biology Insights, Cascade, CO, USA) (23) or AlleleID (Premier Biosoft, Palo Alto, CA, USA) (24) have been applied for probe design in a pathogen characterization experiment (25) . In this article ORMA was used for determining sets of LDR probe pairs in microbiological-related contexts (water safety and food safety applications, respectively). The approach was evaluated and validated using the probe pairs derived from ORMA-determined discriminating positions on a set of cyanobacteria 16S rRNA sequences belonging to 18 different species; the results were compared to those of a previously published study (8) . Secondly, a set of LDR probe pairs for the discrimination of 13 mastitis-or intoxication-related pathogens species in bovine milk was designed and experimentally evaluated. The tool, although here applied on 16S rRNA, can be used on any set of highly correlated sequences.