Sequencing of uncultured microbial communities via both shotgun metagenomic and 16S amplicon methods has provided great insight into the diversity of microbes and their roles in the environment and human health. The most commonly used methods for analysing such datasets are based on identification of Operational Taxonomic Units (OTUs): collections of sequences within a predefined percent nucleotide identity. These OTU ‐ based approaches have some shortcomings, such as ambiguity in OTU definition and limited resolution. In this seminar I will review recent work on alternative approaches to quantifying and comparing microbial community diversity using Bayesian phylogenetic inference. This will include an introduction to basic phylogenetic models and the concepts of alpha and beta diversity in microbial communities.