Haploi is a haplotype inference program for multi-population data. Underlying Haploi is a new haplotype distribution model based on a nonparametric Bayesian model known as the hierarchical Dirichlet process, which represents a tractable surrogate to the coalescent process. It offers a well-founded statistical framework for posterior inference of individual haplotypes, and the size and configuration of haplotype ancestor pools given genotype data.