Mesophillic Thermoproteota were recently placed into a new phylum of Archaea called the Nitrososphaerota (formerly Thaumarchaeota). However there are very few molecular markers that can distinguish this group of archaea from the phylum Thermoproteota (formerly Crenarchaeota). A detailed phylogenetic study using the CSI approach was conducted to distinguish these phyla in molecular terms. 6 CSIs were uniquely found in various Nitrososphaerota, namely Cenarchaeum symbiosum, Nitrosopumilus maritimus and a number of uncultured marine Thermoproteota. 3 CSIs were found that were commonly shared between species belonging to Nitrososphaerota and Thermoproteota. Additionally, a number of CSIs were found that are specific for different orders of Thermoproteota—3 CSIs for Sulfolobales, 5 CSIs for Thermoproteales, lastly 2 CSIs common for Sulfolobales and Desulfurococcales. The signatures described provide novel means for distinguishing Thermoproteota and Nitrososphaerota, additionally they could be used as a tool for the classification and identification of related species.