As microbial ecologists continue to take advantage of high-throughput analytical techniques to describe microbial communities across ever-increasing numbers of samples, the need for new analysis tools that reveal the intrinsic spatial patterns and structures of these populations is crucial. Here we present SitePainter, an interactive graphical tool that allows investigators to create or upload pictures of their study site, load diversity analyses, and display both diversity and taxonomy results in a spatial context. Features of SitePainter include: visualizing alpha diversity, using taxonomic summaries; visualizing beta diversity, using results from multidimensional scaling methods; and animations that show relationships among microbial taxa or pathways over time. SitePainter thus increases the visual power and comprehension of spatially explicit studies. Antonio Gonzalez, Jesse Stombaugh, Christian L. Lauber, Noah Fierer and Rob Knight; Bioinformatics, 2011; doi: 10.1093/bioinformatics/btr685.