Vast genomic databases, low costs of such basic procedures as quantitative PCR, and well-equipped core facilities at most major academic institutions provide excellent conditions for ecologists to integrate molecular tools into ecological studies. Moreover, rapid progress in molecular technologies has made advanced and powerful molecular tools more accessible than ever. Sequencing entire transcriptomes of non-model organisms through next-generation sequencing technology, for example, has become comparable in cost to conducting microarray experiments, and requires little prior knowledge about genomes of the organisms of interest. Another relatively new technology of silencing genes through RNA interference is a clever method of confirming biological significance of differential gene expression. Utilizing these technologies in basic ecological research has enabled scientists to make powerful inferences about genetic mechanisms driving interactions between organisms and the effects of environmental conditions on species interactions. Despite the relative ease, low cost and accessibility of equipment used in molecular research, many ecologists are reluctant to incorporate molecular technologies into their research. Many ecologists are intimidated by the challenges of using molecular tools, but in reality recent advances in these technologies and associated core facilities have made these tools far more accessible to organismal biologists. Thus, we propose a symposium that will provide ecologists with research examples from diverse fields that incorporates molecular tools to answer fundamental questions in ecology. This symposium will contribute to increased knowledge of modern molecular tools by organismal biologists and their applicability to ecological research and will highlight cutting-edge research in this area. It will also stimulate a discussion on the major advantages of using these tools in ecological research and, conversely, on challenges that still hinder integration of molecular biology and ecology. The symposium will be composed of a series of presentations illustrating research that successfully integrates molecular biology and ecology. Among other topics, the symposium will include talks exemplifying the use of molecular technologies in plant-insect interactions, plant ecology and evolution, and insect behavior. We have also invited the director of a core facility to explain the logistics of submitting samples for sequencing, general cost and output generated from next-generation sequencing technologies. Owing to high-throughput nature of sequencing, extracting relevant information can present a significant challenge, and we invited several speakers with expertise in analyzing sequence data to describe methods for approaching sequencing results. A concluding discussion will address the most significant perceived and true obstacles in integrating molecular tools into these ecological studies.