Progress in understanding allelopathic interactions among plants has long been hampered by the complexity of the many direct and indirect interactions involved. Plant processes and growth are not only affected by allelochemicals but by resource limitations, pathogens, herbivores, and microbial interactions. Interference mechanisms frequently interact, and the magnitude of effects can depend on the plant’s biotic and abiotic environment. The rhizosphere is chemically complex, with thousands of potentially bioactive allelochemicals produced by plants, microorganisms and soil invertebrates. The rhizosphere is also dynamic, in that concentrations of these metabolites vary as pulses of allelochemicals are released by plant roots and other organisms, as they leach from decaying plant material, as microorganisms degrade and sometimes transform allelochemicals, and as allelochemicals are taken up by plants, bind to soil components, or leach from the root zone. Recent advancements in instrumentation and technologies for the analysis of trace levels of chemical substances in soil, as well as the development of genomics, proteomics, and transcriptomics approaches allow researchers to probe both the biosynthesis of allelochemicals and plant responses to allelochemical exposures. These new technologies will provide much more detailed information on rhizosphere chemistry and about the production and response to metabolites by individual cells. This review describes case studies and current examples that illustrate how these new approaches and tools can enhance our understanding of allelopathic interactions, and argues that to truly advance our understanding of allelopathic interactions, these must be applied in ecologically rigorous and meaningful ways.