Which genetic markers are used to determine archaea diversity?

Diversity of radA Genes from Cultured and Uncultured Archaea: Comparative Analysis of Putative RadA Proteins and Their Use as a Phylogenetic Marker .... read more

16S rDNA regions can be used to detect both bacterial and archaeal diversity. It's widely used and OK! However, analysis on 16S rDNA regions has limitations and lead to difficulties to discern closely related archaeal species. To increase the analysis resolution, functional genes can be used in phylogenetic studies. read more

Those are characteristics you want for a marker. More details/drawbacks, in comparison to SNPs: The biggest reason for their (initial) popularity is that you only need sequence data to design SSRs, since the repetitive regions are predictable. read more