ChemTree is an interactive, bioinformatics tool designed to explore chemical space and mine the relationships between chemical structure, molecular properties, and biological activity. ChemTree synergistically combines extended connectivity fingerprints and a neighbor-joining algorithm to produce a hierarchical tree with branch lengths proportional to molecular similarity. Compound properties are shown by leaf color, size, and outline to yield a user-defined visualization of the tree. Two representative analyses are included to demonstrate ChemTree's capabilities and utility: assessing dataset overlap and mining structure-activity relationships (SAR).