Results from a high density microarray having 32,392 50-mer oligonucleotides, termed BMS2.1, were analyzed and used for the design of a new slide, called BMS 3.0, with 560 specific oligonucleotides manufactured in standard slides to be used in any open platform. Hybridizations of several samples, either known microorganisms or environmental samples, were performed. Automatic microarray analysis software was built in order to handle these data in a quick an efficient way. While oligonucleotides designed for microorganisms with known genome sequence showed a very good behavior, according to predicted design, variations were detected when different strains were hybridized, probably due to inadequate specificity of probes. Appropriate parameterization of the analysis software will improve prediction of presence for most of the microorganisms.