Since 2005, when the first edition of Molecular Ecology was published, the field has continued to evolve. As a result, this second edition contains numerous updates and additions that reflect the fast-moving pace of genetic discovery. Perhaps the most significant development in molecular ecology in the past five years has been in the area of ecogenomics. In a nutshell, ecogenomics moves away from the more traditional approach of using neutral (non-adaptive) molecular markers to infer patterns of genetic diversity and gene flow, and instead attempts to provide an understanding of adaptive gene functions in an ecological context. We have therefore incorporated into this second edition a new chapter entitled 'Studying Ecologically Important Traits: Ecogenomics, QTLAnalysis, and Reverse Genetics' (Chapter 5). In addition, updates to many other sections of the textbook include explanations of how ecogenomics is being applied to conservation genetics, behavioural ecology and evolutionary biology. Other revisions to this second edition are too numerous to list here, but include discussions of next-generation sequencing, landscape genetics, experimental design and spatial autocorrelation. As before, up-to-date examples are used extensively throughout the text, and are based on studies that have employed a wide range of molecular markers.