Metagenomics is the study of microbial communities using DNA sequencing technologies. Key questions are determining and comparing the taxonomical content of different samples and also their "functional content". This talk will start with a brief introduction to the field. We will then discuss one approach to the problem that uses database comparison and tree-based algorithms to place DNA sequence reads into the NCBI taxonomy, as implemented in our metagenomic analysis tool MEGAN. We will then discuss the problem of comparing different metagenomic datasets and ask how one might best include phylogenetic methods to identify species in a sample.