Plants assimilate inorganic nitrogen absorbed from soil into organic forms as Gln and Glu through the glutamine synthetase/glutamine:2-oxoglutarate amidotransferase (GS/GOGAT) cycle. Whereas GS catalyzes the formation of Gln from Glu and ammonia, GOGAT catalyzes the transfer of an amide group from Gln to 2-oxoglutarate to produce two molecules of Glu. However, the regulatory role of the GS/GOGAT cycle in the carbon-nitrogen balance is not well understood. Here, we report the functional characterization of the rice ABNORMAL CYTOKININ RESPONSE 1 (ABC1) gene that encodes an Fd-GOGAT. Whereas the weak mutant allele abc1-1 mutant shows a typical nitrogen-deficient syndrome, the T-DNA insertional mutant abc1-2 is seedling lethal. Metabolomics analysis revealed the accumulation of excessive amount of amino acids with high N/C ratio (Gln and Asn) and several intermediates in the tricarboxylic acid cycle in abc1-1, suggesting that ABC1 plays a critical role in regulating nitrogen assimilation and carbon-nitrogen balance. Five non-synonymous single nucleotide polymorphisms were identified in the ABC1 coding region and characterized as 3 distinct haplotypes, which have been highly and specifically differentiated between japonica and indicasubspecies. These results suggest that ABC1/OsFd-GOGAT is essential for plant growth and development by modulating nitrogen assimilation and the carbon-nitrogen balance.