Program PARTITION is software for hierarchical partitioning of species diversity data from ecological studies and biodiversity surveys. PARTITION can be used on balanced and unbalanced hierarchical designs with up to six levels of sampling. Version 3 of the program calculates partitions of species richness and Hill’s Q-diversity metrics. The program conducts randomization tests to determine whether the observed diversity partitions are statistically different from those expected by chance. PARTITION was developed with funding from the National Science Foundation (DEB 0203569). PARTITION runs on Microsoft Windows® 2000, XP, or Vista operating systems.