aflpdat is a collection of R functions that facilitates the handling of dominant genotypic data. It converts data from a standard tab-separated table to the input formats of the following programs: arlequin, structure, treecon, paup and hickory. In addition, it calculates the proportion of polymorphic markers in each population, and estimates gene diversity as the average proportion of pairwise differences between individuals with confidence intervals based on bootstrapping across markers. It also produces summary tables of marker frequencies and the presence or absence of markers in each population. aflpdat can be downloaded from http://www.nhm.uio.no/ncb/.