We have studied the catalytic effects of peroxomolybdates, i.e., [MoO(O2)2(OH)(H2O)]-, on hydrogen peroxide bleaching on hardwood and softwood pulps in terms of kappa number reduction, hexeneuronic acid (HexA) removal, and delignification. We found that, in the case of hardwood pulp, the decrease of HexA in the peroxomolybdate bleaching stage corresponds to more than 60% of the kappa number reduction obtained in that stage. In the case of pine pulp, inclusion of molybdate in the peroxide stage lowered the kappa number by 4.1. This work also shows that hydrogen peroxide, in the absence of molybdate, did not react to any noticeable extent with neither the lignin model compounds or HexA, under otherwise similar conditions. In order to investigate the oxidation mechanism, lignin model compounds with different side chain structures were reacted with peroxomolybdate. 1H-NMR revealed that lignin model compounds with double bond structure in conjugation with the aromatic ring has an extreme fast speed to react with the peroxomolybdate catalysts systems, presumably through hydroxylation reactions. This mechanism was supported by XPS analysis of the pulp samples, in which the activated hydrogen peroxide was found to act in a similar fashion on surface lignin as well. In conclusion, molybdate activated hydrogen peroxide can be considered a very efficient and selective bleaching agent.