Cells of land plants contain several kinds of plastids such as chloroplasts, etioplasts, proplastids, leucoplasts, and amyloplasts. Among them, the chloroplast, the most well characterized type of plastid, relies on expression of plastid-encoded photosynthetic genes. The genome of plastids encodes many photosynthetic genes that are mainly transcribed by the plastid-encoded plastid RNA polymerase (PEP). Transcriptional activity of PEP is controlled by nuclear-encoded sigma factors that are important for transcription initiation and promoter selectivity. Arabidopsis thaliana possesses 6 sigma factor genes, SIG1 to 6. Here, we analyzed the function of SIG6, a gene related to chloroplast differentiation. The null mutant (sig6-1) of the SIG6 gene exhibited a pale green phenotype in the cotyledons and in the basal part of emerging true leaves at early stages of development. Interestingly, as leaves matured, the color of cotyledons and true leaves changed to green. In the wild-type and sig6-1 mutant, plastids visualized by green fluorescent protein (GFP) were observed under the epifluorescence microscope. In cotyledons of 3-day-old seedlings, chloroplasts of the sig6-1 mutant showed small and irregular morphology compared with that of the wild-type chloroplasts. However, amyloplasts and leucoplasts in root tissues showed no obvious differences between the wild-type and the sig6-1 mutant. These results suggest that SIG6 plays a key role during the early stages of chloroplast differentiation, but not in differentiation into other types of plastids such as leucoplasts and amyloplasts.