Biodiversity—the sum of life and its organizational patterns from genes to the biosphere—is one of humanity’s most important natural resources. A major objective of contemporary ecology research is to understand how biodiversity affects trophic interactions within communities and the functioning of ecosystems. Such research is dependent upon accurate taxonomic identification and quantification of species within the studied system. However, the number of taxonomists has declined in recent decades creating a problem for ecologists studying biodiversity. We propose the term “applied taxonomy” to describe a new field that may help reinvigorate taxonomic work for the explicit purpose of contributing to community and ecosystem ecology. In our presentation, we will discuss the current challenges and opportunities that ecologists and taxonomists face in the search for accurate and meaningful methods to study the interactions and functions of species within communities and ecosystems. We will highlight the need to reorganize aspects of taxonomy into a new field that can be applied to the rapid assessment of biodiversity in many types of ecological research. This approach is needed to develop species conservation and ecosystem management plans that will result in a more sustainable biosphere.