The present study was undertaken to clarify the change of induction of CYP4M5 and CYP4M9 expression level by rutin. In this study, we used dual-spike-in qPCR to examine expression profiles of the silkworm Bombyx mori CYP4M5 and CYP4M9 genes in the larval midgut and fatbody after exposure to rutin. In organization-course study, rutin at middle concentration (5×10-2ng/µL) caused significant upregulation of CYP4M5 and CYP4M9 genes at early time point (2h) in fatbody, higher concentration (5×10-1ng/µL) did secondly, while lower concentration (5×10-3ng/µL) caused little change. In the midgut of silkworm, rutin in all concentrations didn't affect the expression of the two genes. These findings showed that induction of CYP4M5 and CYP4M9 expression level by rutin are concentration depended and tissue-specific.Collectively, CYP4M5 and CYP4M9 genes may have some relationships with metabolism of rutin in silkworm.