Background/Question/Methods Microbial ecologists have long recognized the value of a phylogenetic perspective on diversity, due in part to the challenges of taxonomic classification and species delimitation in microbes. The increasing availability of metagenomic data from environmental shotgun sequencing offers the potential to revolutionize our understanding of ecological communities, and will likely drive the development of a new conceptual framework for understanding biological diversity that focuses on patterns of relatedness among individual organisms rather than on classical taxonomic ranks such as species. I give an overview of the conceptual and practical challenges of working with metagenomic data, and present a metagenomic analysis of diversity along spatial and environmental gradients in marine microbial communities. Results/Conclusions I present an analysis of diversity in a marine microbial metagenomic data set. I identified sequences belonging to thirty protein encoding marker gene families in this dataset, and constructed a phylogenetic hypothesis for each gene family using several tree inference methods. Based on these phylogenies, as well as measures of taxonomic diversity based on estimates of OTU richness in environmental samples, I show that taxonomic and phylogenetic diversity vary independently along spatial and environmental gradients in these communities. Phylogenetic diversity and turnover generally showed stronger relationships with spatial and environmental gradients of depth, temperature and water chemistry than did their taxonomic equivalents. The nature of diversity-environment relationships differed depending on the gene family used to estimate phylogenetic diversity. I discuss the implications of these findings for our understanding of the ecology and evolution of diversity in microbial communities.