Issues to explore in genotypic datasets include the number and characteristic patterns of subpopulations and, possibly, relationships among them. Model-based clustering methods have been adopted to find a number of clusters and the individual assignments. However, they cannot infer genetic relationships among subpopulations the way phylogenetic trees, e.g., the widely-used Neighbor-Joining (NJ) tree, can. In this paper we propose an unsupervised, iterative clustering framework called iNJclust. It performs clustering on an NJ tree with a graph-based partitioning technique. The iterative process enhances the zooming ability and corrects the topology of the final NJ trees. Inference on genetic similarities between subpopulations is also possible. As final outputs, the iNJclust algorithm provides an estimate of the number of clusters, individual assignments, a population tree, as well as sub-trees of the terminal nodes. We illustrate the superior clustering performance of the proposed algorithm using Human 27 populations, bovine 47 breeds, and sheep 28 breeds datasets. © 2012 ICPR Org Committee.