As conservation genetics is integrated into multipurpose forest management, questions regarding the genetic effects of silviculture arise. Careful harvesting regimes, using natural regeneration, could preserve genetic resources within commercially important species, both in reserves and in logged areas. We investigated the effects of two natural regeneration methods, shelterwood and group selection cutting, on subsequent pollen movement and mating system in four native stands of monospecific Scots pine (Pinus sylvestris L.) in the Guadarrama Chain of central Spain. Using TwoGener analysis, we estimated an average pollination distance of 17–22 m and a relatively large effective number of pollen donors (Nep>70). We found a non-significant trend toward increasing pollination distance and larger effective number of pollen donors, subsequent to cutting. Considering the high conspecific density of the stands we studied (80–315 trees/ha), pollen dispersal estimates seem consistent with values from other studies, using other methods. Mating system analysis, using the MLTR mixed-mating model, showed high outcrossing rates for all four stands (tm=0.93–0.99), but failed to show significant effects of stand thinning, although slight increases of the outcrossing rate and the apparent rate of consanguineous mating (tm–ts) occurred, subsequent to cutting. Results suggest that the pollination system of Scots pine is resilient enough to preclude a negative impact of natural regeneration cutting. From the pollination point of view, normal Scots pine silvicultural systems seem compatible with genetic conservation purposes in central Spain.