Mutations in Phytochrome Interacting Factors (PIFs) induce a conversion of the endodermal amyloplasts necessary for gravity sensing to plastids with developed thylakoids accompanied by abnormal activation of photosynthetic genes in the dark. In this study, we investigated how PIFs regulate endodermal plastid development by performing comparative transcriptome analysis. We show that both endodermal expression of PIF1 and global expression of the PIF quartet induce transcriptional changes in genes enriched for nuclear-encoded photosynthetic genes such as LHCA and LHCB. Among the 94 shared differentially expressed genes identified from the comparative transcriptome analysis, only 14 genes are demonstrated to be direct targets of PIF1, and most photosynthetic genes are not. Using a co-expression analysis, we identified a direct target of PIF, whose expression pattern shows a strong negative correlation with many photosynthetic genes. We have named this gene REPRESSOR OF PHOTOSYNTHETIC GENES1 (RPGE1). Endodermal expression of RPGE1 rescued the elevated expression of photosynthetic genes found in the pif quadruple (pifQ) mutant and partly restored amyloplast development and hypocotyl negative gravitropism. Taken together, our results indicate that RPGE1 acts downstream of PIF1 in the endodermis to repress photosynthetic genes and regulate plastid development.