The availability of molecular genetic markers coupled with advanced statistical estimation procedures have significantly increased our ability to estimate gene flow rates and other population parameters for many plant species. The improved ability to accurately estimate gene flow into plant populations allows us to predict the genetic consequences of small population size, habitat fragmentation, and isolation distance. However, when gene flow is estimated in conjunction with male reproductive success or effective population sizes, some problems can arise. For example, when estimating male reproductive success in populations that experience high rates of gene flow, the assignment of progeny to certain pollen donors may be biased towards individuals with multi locus genotypes that most closely approximate gene frequencies in the immigrant donor population. Perhaps a more serious problem is the observation that individual trees do not sample the pollen pool at random as is assumed by most estimation procedures. There is considerable evidence from the plant mating system literature that individual maternal trees often receive genetically different pollen. This is probably also true of pollen that immigrates into a population. Thus, a second generation of gene flow estimation procedures are needed that can take into account such heterogeneity in the immigrant pollen pool and use iterative procedures to better estimate the immigrant pollen pool for individual trees as well as populations.