Casbene synthase is responsible for the first commited step in the biosynthesis of phorbol esters (PE) in the Euphorbiaceae. PE are abundant in the seeds of the biofuel crop Jatropha curcas and its toxicity precludes the use of the protein-rich cake obtained after oil extraction as an animal feed and the toxicity of the fumes derived from burning PE containing biofuel is also a matter of concern. This toxicity is a major hindrance to exploit the potential of this crop as a source of raw material for the production of biodiesel. For this reason, current research on J. curcas is mainly focused in the understanding of the biosynthesis and site of synthesis of PE, as an avenue for the development of biotechnological of genotypes unable to synthesize PE in its seeds. Here, we present the results of targeted proteome assays (SRM and PRM) to monitor and quantify casbene synthase in leaves, endosperma and roots of two J. curcas of contrasting levels of PE. The assays were based in the use of synthetic isotopic labeled peptides derived from 12 gene models of casbene synthase from the J. curcas genome and results showed the presence of casbene synthase encoded in seven of the 12 gene models. Several specific transitions were identified and which can be used to monitor several casbene synthase proteins by any one of the two targeted proteomics assays and/or to validate the results of transcription-based experiments.