Petal pigmentation is the most important aspect in natural flower coloration. In the present study, the inhibition of petal pigmentation by exogenous ammonium was investigated. Ray floret petals detached from inflorescences of Gerbera hybrida (Shenzhen No. 5) were cultured in vitro on media supplied with different forms of nitrogen and its assimilated compounds. The expression of a set of genes involved in anthocyanin biosynthesis and regulation was determined by Northern blotting assay. It was found that ammonium (NH4+), not nitrate (NO3-), in millimolar concentrations inhibited anthocyanin accumulation. The expressions of Gerbera chalcone synthase 1 (GCHS1), Gerbera chalcone synthase 2 (GCHS2) and Gerbera dihydroflavonol-4-reductase (GDFR) decreased, while six other related genes showed no significant changes after NH4+ treatment. Further studies on NH4+ function indicated that glutamine (Gln) acted as a downstream factor of NH4+ to suppress petal pigmentation. Both exogenous Gln and NH4+ were found to inhibit anthocyanin accumulation in the petals, and the application of Gln was also found to inhibit the expressions of GCHS1, GCHS2 and GDFR. The application of NH4+ also resulted in an increase in the activity of Gerbera glutamine synthetase (EC 6.3.1.2) along with a rapid increase of Gln content. When methionine sulfoximine, an inhibitor of glutamine synthetase (GS), was added, it was found to block the NH4+-induced inhibition of pigmentation. From these experiments, we conclude that the NH4+-induced suppression of petal pigmentation is not because of NH4+ toxicity, and the inhibition of pigmentation caused by the addition of exogenous NH4+ is the result of its assimilation into Gln.