Any variable region of a genome is good for distinguishing between closely related organisms.  If a region is not under strong negative selection (most mutations lethal or detrimental) the sequence drifts as mutations accumulate.  But many other considerations are also involved with choosing one variable region as being very good for identifying what type of organism is in your sample.  One of the considerations is having the variable region flanked by highly conserved regions so that it is easy to design PCR primers and sequencing primers that will work across a wide variety of organisms.  Another consideration is having a reasonable size of the variable region such as something between 50 and 1,000 bases length which makes PCR and sequencing inexpensive and reliable.  A third major consideration is having many groups of researchers all agree to use the same region, so that if I sequence a region from my organism I can compare it to thousands of other organisms.  The database of 16S sequences in huge, and there has been an effort to sequence 16S from a very wide variety of different bacteria.

Any variable region of a genome is good for distinguishing between closely related organisms.  If a region is not under strong negative selection (most mutations lethal or detrimental) the sequence drifts as mutations accumulate.  But many other considerations are also involved with choosing one variable region as being very good for identifying what type of organism is in your sample.  One of the considerations is having the variable region flanked by highly conserved regions so that it is easy to design PCR primers and sequencing primers that will work across a wide variety of organisms.  Another consideration is having a reasonable size of the variable region such as something between 50 and 1,000 bases length which makes PCR and sequencing inexpensive and reliable.  A third major consideration is having many groups of researchers all agree to use the same region, so that if I sequence a region from my organism I can compare it to thousands of other organisms.  The database of 16S sequences in huge, and there has been an effort to sequence 16S from a very wide variety of different bacteria.

As 16s rDNA is highly conserved gene seq. throughout the bacterial domain. 16s gene contains varibale and conserved region. Among the variable regions of 16s gene v3 is highly variable region which can distinguish bacterial subtypes on dgge if amplicon contains this v3 region rest part of the gene is highly conserved. So closeley related bacteria cant be distinguished by banding pattern on gel. So distinguish among closely related bacteria amplicon must contains hyper varibale regions.

Check out Figure 1 in this paper for the variability of the different V regions in 16S/18S:

https://www.researchgate.net/publication/46094759_V-Xtractor_an_open-source_high-throughput_software_tool_to_identify_and_extract_hypervariable_regions_of_small_subunit_%2816S18S%29_ribosomal_RNA_gene_sequences

Article V-Xtractor: An open-source, high-throughput software tool to...