Abstract: A universal primer pair (SEQ. ID 1 and 2) is used to amplify total organismal DNA in a sample. Probes from any or all three taxonomic domains may be used to further classify the amplified DNA by organelle (e.g., chloroplast) or by taxonomic DNA levels (i.e., kingdom, phylum, class, order, or family) in relation to total DNA. The universal primer pair amplifies regions of the 16s (eukaryotic 18s) ribosomal DNA gene by hybridizing to regions highly conserved among all organismal DNA. Less conserved regions within the amplicon produced by the universal primers are targeted by probes, so that a general taxonomic breakdown of the DNA present can be determined. The primers and probes of the present invention are conveniently used with real-time PCR or similar or related technology to detect and enumerate any organismal DNA from the three major taxonomic groups (bacteria, archaea and eucarya) and enable improved methods of environmental surveillance and quick identification of unknown biological material.