The increasing availability of large genomic datasets as well as the advent of Bayesian phylogenetics facilitate the investigation of phylogenetic incongruence, which can result in the impossibility of representing phylogenetic relationships using a single tree. While sometimes considered as a nuisance, phylogenetic incongruence can also reflect meaningful biological processes as well as relevant statistical uncertainty, both of which can yield valuable insights in evolutionary studies. We introduce a new tool for investigating phylogenetic incongruence through the exploration of phylogenetic tree landscapes. Our approach, implemented in the R package treespace, combines tree metrics and multivariate analysis to provide low dimensional representations of the topological variability in a set of trees, which can be used for identifying clusters of similar trees and group‐specific consensus phylogenies. treespace also provides a user‐friendly web interface for interactive data analysis. treespace is integrated alongside existing standards for phylogenetics and is easily accessible through a web interface. It fills a gap in the current phylogenetics toolbox in R and will facilitate the investigation of phylogenetic results. This article is protected by copyright. All rights reserved.