Chemically mediated interactions between organisms influence ecosystem structure, making it crucial for ecologists to understand these interactions. Advances in chemical ecology have often been closely linked to advances in analytical chemistry techniques. One recent development is the use of metabolomics to address questions in chemical ecology. Although metabolomics has much to offer this field, it is not without drawbacks. Here we consider how metabolomics techniques can supplement the traditional bioassay-guided fractionation approach to chemical ecology. We focus on specific examples that illustrate the advantages that metabolomic methods can provide over other methods in order to understand chemically mediated interactions between organisms.