The assignment of peroxo stretching frequencies for Molybdenum and Tungsten complexes is studied by DFT and MP2 calculations. We found that M06 functional is unsuitable for assignment of Mo=O and O–O stretches in CpMo(η2-O2)OCH3 and we found that MP2 and even the def2-TZVP do not give accurate order of asymmetric and symmetric Mo=O stretching. We recommend the M06L, which is a good compromise between speed and accuracy, for works involving these complexes. For a series of ten Molybdenum and Tungsten complexes studied we found that, for Mo/W=O stretching frequencies at M06L/def2-TZVP, after scaling, a small RMSD of 15 cm−1 could be obtained. However peroxo stretching frequencies RMSD remains high at 40 cm−1 after scaling. This could potentially point out the need for reassignment of experimental peroxo frequencies in some of the works cited in this report.