HIV patients form clusters in HIV transmission networks. Accurate identification of these transmission clusters is essential to effectively target public health interventions. One reason for clustering is that the underlying contact network contains many local communities. We present a new maximum-likelihood method for identifying transmission clusters caused by community structure, based on phylogenetic trees. The method employs a multi-state birth–death (MSBD) model which detects changes in transmission rate, which are interpreted as the introduction of the epidemic into a new susceptible community, i.e. the formation of a new cluster. We show that the MSBD method is able to reliably infer the clusters and the transmission parameters from a pathogen phylogeny based on our simulations. In contrast to existing cutpoint-based methods for cluster identification, our method does not require that clusters be monophyletic nor is it dependent on the selection of a difficult-to-interpret cutpoint parameter. We present an application of our method to data from the Swiss HIV Cohort Study. The method is available as an easy-to-use R package.