Currently microorganism are best identified using 16S rRNA and 18S rRNA gene sequencing. The sequencing is considered to be the "gold standard" nowadays. The disadvantage, at least for the clinical microbiology laboratories, is that it's quite laborious, time-consuming and not very cheap.

16S ribosomal RNA (or 16S rRNA) is the component of the 30S small subunit of a prokaryotic ribosome that binds to the Shine-Dalgarno sequence. The genes coding for it are referred to as 16S rRNA gene and are used in reconstructing phylogenies, due to the slow rates of evolution of this region of the gene (Wikipedia).