Next-generation sequencing has revolutionized ecology and evolutionary biology enabling genome-wide studies of genetic diversity and gene expression to understand how species adapt to current environments and respond to global change. In multi-species contexts, we now have the tools to understand the importance of interspecific gene flow in adaptation, determine the role of genetic diversity in community composition, and characterize the diversity and function of cryptic organisms, such as microbes, in communities and ecosystems. This course covers key topics in ecological genomics at the individual, population, interspecific, community and ecosystem levels. The course consists of lectures, student-led discussions of primary literature on genomic applications to contemporary environmental problems, and hands-on experience manipulating and analyzing real genomic data sets with the latest bioinformatic tools in UNIX/Linux and R.