In chloroplasts ferredoxin:NADP(H) oxidoreductase (FNR) enzymes oxidize the final reduced product of the photosynthetic electron transport chain, ferredoxin (Fd), to reduce NADP+, and play a role in cyclic electron transport. Oppositely, in non-photosynthetic plastids FNR oxidizes NADPH to provide reduced Fd for enzymes of bioassimilation and biosynthesis. These separate plastid types predominantly contain different iso-proteins, with distinct leaf FNR (LFNR) and root FNR (RFNR) features. Genomic and transcript information has identified multiple isoforms of both LFNR and RFNR in several species. We have used a technique for rapidly purifying Fd-interacting proteins from Arabidopsis thaliana to identify the two LFNR and two RFNR proteins encoded in the genome. Analysis of purified LFNRs revealed variation in pI and in abundance between stromal and thylakoid fractions of chloroplasts. Transcript and protein levels of the two LFNRs were similar in leaves, but varied in relative abundance between stems and siliques and in response to different nitrogen growth regimes. Relative transcript accumulation and protein abundance of the two RFNR isoforms varied between organs and in response to different nitrogen growth regimes. These results show that the multiple FNR iso-proteins of A. thaliana have variable metabolic roles and contribute differentially to nitrogen assimilation.