Enzymatic machinery fundamental for cell-functioning in Archaea, such as the DNA- directed RNA polymerase (RNAP), is a simplified version of its eukaryotic counterpart. This is clearly noticeable in the conservation of sequence and structure of corresponding enzymes. Post translational modifications (PTMs) often serve as functional regulatory factors for various enzymes and complexes, both in Eukarya and Archaea. Among the various PTMs, methylation and acetylation have been recently attracting most attention. Nevertheless, little is known about such PTMs in Archaea, and cross-methodological studies are scarce. We examined methylation and N-terminal acetylation of endogenously purified crenarchaeal RNA polymerase from Sulfolobus shibatae and Sulfolobus acidocaldarius. In-gel and in-solution protein preparation methods were combined with collision-induced dissociation (CID) and electron-transfer dissociation (ETD) mass spectrometry analysis. Overall, 20 and 27 methyl-lysines for S. shibatae and S. acidocaldarius were identified, respectively. Furthermore, two N-terminal acetylation sites for each of these organisms were assessed. As a result, we generated a high-confidence dataset for the mapping of methylation and acetylation sites in both Sulfolobus species, allowing comparisons with the data previously obtained for RNAP from Sulfolobus solfataricus. We confirmed that all observed methyl-lysines are on the surface of the RNAP.