We introduce ColorTree, a simple yet powerful batch customization tool for phylogenic trees. Based on pattern matching rules, ColorTree applies a set of customizations to an input tree file, e.g., coloring labels or branches. The customized trees are saved to an output file, which can then be viewed and further edited by Dendroscope (a freely available tree viewer). ColorTree runs on any Perl installation with BioPerl as a stand-alone command line tool, and its application can thus be easily automated. Besides the raw perl script, we also provide pre-compiled executables for a variety of operating systems. This way, hundreds of phylogenic trees can be customized for easy visual inspection in a matter of minutes.