aflpop is a population allocation and simulator program based on amplified fragment length polymorphism markers. The allocation method is an adaptation of Paetkau's method for co-dominant alleles. Besides population allocation of specimens of unknown origin, re-allocation of sample genotypes, as well as allocation of artificial (Monte Carlo) specimens, may be run to estimate expected rates of correct allocations. Thanks to its embodied simulator, aflpop can provide information on the rates and types of incorrect allocations and on empirical distributions of likelihood statistics. A filtering procedure within aflpop allows the selection of loci according to user-defined criteria.