Multicellular organisms, whether plant or animal, coordinate their growth and development and many responses to the environment by using small signaling molecules for communication between cells or organs. The established plant hormones include auxin, cytokinin, gibberellin, brassino-steroids, abscisic acid (ABA), and jasmonic acid (JA), which mediate numerous physiological and biochemical responses. However, in comparison to animal systems, our knowledge about the molecular mechanisms of hormone perception and signaling in plants is still fragmentary, despite the success of identifying receptors for several of these highly active compounds, e.g. auxin, cytokinin, gibberellin, and brassinosteroids. Other receptors remained elusive or in question, namely those for JA and ABA, and candidate binding proteins for these hormones were only recently identified. Here we first summarize the initial research on JA biosynthesis, metabolism and action, which identified important regulatory nodes and signaling intermediates, and then concentrate on describing methods and experimental approaches that eventually lead to the identification of proteins having the capacity to bind and/or convert jasmonates. We discuss advantages and problems of in vitro and in vitro methods for receptor identification, including application of JA derivatives to elucidate structure-function relationships, genetic screens or expression profiling. Finally, we present an alternative method for identifying direct targets of small molecules, the yeast three-hybrid system, which allows direct functional cloning of proteins that interact with synthetic hybrid ligands in vivo. First candidate proteins isolated by using different JA- and ABA-based hybrid ligands are presented and discussed.