The gas-phase interactions of uracil and thymine with alkylmercury cations, in particular [CH₃Hg]⁺, n-BuHg⁺ and t-BuHg⁺, were studied through the use of electrospray ionization coupled to tandem mass spectrometry. We observed that the interaction of akylmercury compounds with the nucleobases (NB) gives rise to a single type of complex of general formula [RHg(NB)]⁺, except for t-butyl-mercury (no interaction). The subsequent MS/MS experiments show that the [RHg]⁺ ions (R = Me, n-Bu) exhibit a peculiar reactivity characterized by the transfer of the alkyl group to the nucleobases. Indeed, the main fragmentation process observed leads to the loss of neutral Hg, producing [(NB)R]⁺ ions. Only when the length of the alkyl chain increases, as in the case of reactions with [n-BuHg]⁺, a new fragmentation path is opened, yielding the protonated nucleobase, [(NB)H]⁺, with the concomitant elimination of 2 C₄H₄ + Hg. A thorough analysis of the mechanisms behind both dominant processes was carried out through the use of Infrared Multiple Photon Dissociation (IRMPD) in the fingerprint region, combined with an analysis of the corresponding potential energy surfaces by using high-level density functional theory (DFT) calculations.