Drosophila rhodopsin consists of an apoprotein, opsin, and a chromophore, 11-cis-3-hydroxyretinal. When flies are raised in carotenoid-free medium, rhodopsin transport is blocked between the rough endoplasmic reticulum (rER) and the Golgi body, and immature opsin accumulates in the rER. To elucidate how carotenoid controls the protein transport between these organelles, we investigated the morphological and molecular-biological defects caused by carotenoid deprivation. The results demonstrated that this deprivation causes rER elongation and a shortening of the rhabdomeric microvilli, whereas the density and morphological features of the Golgi body are not significantly affected. Moreover, the content of rhabdomeric proteins other than rhodopsin is not decreased by the deprivation. These results indicate that carotenoid deprivation does not affect the overall traffic of vesicle transport, but selectively suppresses rhodopsin transport between the rER and the Golgi body. We further investigated the gene and protein expression of Rab proteins that control the vesicle transport between cell organelles. The results demonstrated that neither gene nor protein expression of RAB1 and RAB2 is influenced by carotenoid deprivation, which also supports the above conclusion.