Assessment of contemporary pollen-mediated gene flow in plants is important for various aspects of plant population biology, genetic conservation and breeding. Here, through simulations we compare the two alternative approaches for measuring pollen-mediated gene flow: (i) the neighborhood model — a representative of parentage analyses, and (ii) the recently developed twogener analysis of pollen pool structure. We investigate their properties in estimating the effective number of pollen parents (Nep) and the mean pollen dispersal distance (δ). We demonstrate that both methods provide very congruent estimates of Nep and δ, when the methods’ assumptions considering the shape of pollen dispersal curve and the mating system follow those used in data simulations, although the neighborhood model exhibits generally lower variances of the estimates. The violations of the assumptions, especially increased selfing or long-distance pollen dispersal, affect the two methods to a different degree; however, they are still capable to provide comparable estimates of Nep. The neighborhood model inherently allows to estimate both self-fertilization and outcrossing due to the long-distance pollen dispersal; however, the twogener method is particularly sensitive to inflated selfing levels, which in turn may confound and suppress the effects of distant pollen movement. As a solution we demonstrate that in case of twogener it is possible to extract the fraction of intraclass correlation that results from outcrossing only, which seems to be very relevant for measuring pollen-mediated gene flow. The two approaches differ in estimation precision and experimental efforts but they seem to be complementary depending on the main research focus and type of a population studied.