MOTIVATION Microbial community profiling is a highly active area of research, but tools that facilitate visualization of phylogenetic trees and associated environmental data have not kept up with the increasing quantity of data generated in these studies. RESULTS TopiaryExplorer supports the visualization of very large phylogenetic trees, including features such as the automated coloring of branches by environmental data, manipulation of trees and incorporation of per-tip metadata (e.g. taxonomic labels). AVAILABILITY http://topiaryexplorer.sourceforge.net. CONTACT firstname.lastname@example.org.