The differentiation between gram negative and gram positive bacteria was investigated based on the identification of specific sequences in the 16S rRNA of pathogenic bacteria. The rRNA sequences were aligned and detection probes were identified using the AlleleID software. Subsequently, the specificity of the probes was checked using the basic local alignment sequence tool of the NCBI data bank. One 23 nt long probe sequence was identified that is able to bind to 79% of the selected gram negative bacteria where as the gram positive probe can only detect 64% of the selected gram positive bacteria. Unfortunately, it was impossible to identify a second probe that was specific and common to all gram negative and even less for all gram positive bacteria. Further experiment will be conducted to test the sensitivity of the probes and their limits of detection.