The insect midgut has remarkable similarities with the vertebrate intestine especially concerning controlling cell regulation by the stem cells. While the formation of the pupal midgut from stem cells is regulated by ecdysone, it is inhibited by juvenile hormone via suppression of ecdysone release. This study investigated the possible functions of ecdysone-related genes in the stem cells of Bombyx mori L., 1758 (Lepidoptera: Bombycidae) during larval-pupal metamorphosis. The study was conducted in the Ege University silkworm culture laboratory and insect physiology research laboratory during the years between 2014-2018. Juvenile hormone analogue, fenoxycarb was applied to the fifth instar Bombyx larvae to delayed or inhibit the formation of the pupal midgut. Morphologic observations were performed by hematoxylin plus eosin staining; the proliferation rate of stem cells was analyzed by bromodeoxyuridine cell proliferation assay and expression patterns of ecdysone-related genes were detected by quantitative real-time reverse transcriptase-polymerase chain reaction. Expression states of genes and developmental events of the midgut were differently affected by fenoxycarb treatment in an application time-dependent manner. According to results, genes were firstly classified based on their sensitivity of fenoxycarb, then grouped according to their expression profile in connection with morphological evaluations of stem cells.