Ferredoxins (Fds) play a unique and important role in photosynthetic electron transport. Recently, we characterized the function of Fd1 in rice (Oryza sativa L.), showing that Fd1 is the primary photosynthetic electron transport protein and that Fd1 participates in carbon assimilation. However, the subcellular localization and specific functions of other Fds in rice are not yet fully understood. Here, our subcellular localization analysis of the seven Fds in rice showed that they are located in the chloroplasts of photosynthetic tissues and the plastids of non-photosynthetic tissues. Moreover, qRT-PCR indicated that Fd1 transcript levels were highest in photosynthetic tissues, while Fd4 transcript levels were highest in non-photosynthetic tissues. Collectively, our results suggest that rice Fds are located in chloroplasts/plastids, but may function in different tissues, and Fd4 may be a non-photosynthetic type Fd.