Microbial communities are complex and so are the data we use to describe them. In this chapter, we analyze a 16S amplicon data set from a marine time series using the open source QIIME software package. We first summarize complex, multivariate community composition data using ordination techniques. We then use the insights gained from ordination and multivariate statistical techniques to characterize the dominant relationships between environmental parameters and the microbial community in this marine ecosystem. Finally, we identify a list of taxa that show significant changes in relative abundance across seasons and describe the relationship between seasonality and community diversity. We go over several data visualization techniques that allow us to interpret our results. Analysis notes, QIIME commands, and sample data are provided. Finally, we discuss caveats regarding correlations and relative abundance data and describe how the statistical tools used in our 16S amplicon example can be applied to other types of “omics” data sets.