The program package TreeLD implements a unified approach to association mapping and fine mapping of complex trait loci and a novel approach to visualizing association data, based on an inferred ancestry of the sample. Fundamentally, the TreeLD approach is based on the idea that the evidence for association at a particular position is contained in the ancestral tree relating the sampled chromosomes at that position. TreeLD provides an easy-to-use interface and can be applied to case-control, TDT trio and quantitative trait data.