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Backgrounds Limonoids, a major bioactive components, are produced by triterpenoids metabolic pathway. So far, the detailed biochemical reactions regarding to limonoid biosynthesis and their molecular regulation remain elusive. The identification of transcription factors that regulate limonoids biosynthetic pathways is not only necessary for understanding the regulatory mechanisms but also as a tool for manipulating biosynthetic genes for biotechnological applications.Results In this study, CiMYB42 transcription factor was isolated and identified. Multiple alignment analysis and phylogenetic analysis demonstrated that CiMYB42 is a typical R2R3MYB transcription factor and its amino acid is similar to that of AtMYB42 . The limonoids content was higher in the citrus sinensis and citrus grandis than other species. The diverse accumulation patterns also showed in different leaf developmental stages. Expression of CiMYB42 was significantly related to limonoids content and the expression of CiOSC in some of citrus varieties. CiMYB42 transgenic sweet orange resulted significantly change on limonoids contents. Noticeably, CiMYB42 -RNAi induced dwarf phenotype and mainly decreased nomilin accumulation. Overexpressing CiMYB42 mainly increased limonin content. Yeast one hybrid assay results indicated that CiMYB42 exclusively bind to the promoter of CiOSC. In brief, CiMYB42 involved in the limonoids biosynthesis through binding the promoter of CiOSC in citrus.Conclusions These results indicated that CiMYB42 is an important transcription activator involved in limonoids biosynthesis by regulating the expression of CiOSC . This is the first report elucidating the role of transcription factor in citrus limonoids biosynthesis. Our contributions will provide a reference to understanding regulatory mechanisms of R2R3MYB TFs in the triterpenoids biosynthetic pathway.