Dehydration-responsive element-binding (DREB) transcription factors (TFs) are key regulators of stress-inducible gene expression in plants. Anthocyanins, an important class of flavonoids, protect plants from reactive oxygen species produced under abiotic stresses. However, regulation of DREBs on anthocyanin accumulation is largely unknown. Here, an A-5 subgroup DREB gene (AmDREB3) isolated from Ammopiptanthus mongolicus, a desert broadleaf shrub with very high tolerance to harsh environments, was characterized in terms of both abiotic stress tolerance and anthocyanin accumulation. AmDREB3 does not contain the transcriptional repression motif EAR, and the protein was located in the nucleus and has transcriptional activation capacity. The transcription of AmDREB3 was differentially induced in the shoots and roots of A. mongolicus seedlings under drought, salt, heat, cold, ultraviolet B, and abscisic acid treatments. Moreover, the transcript levels in twigs, young leaves, and roots were higher than in other organs of A. mongolicus shrubs. Constitutively expressing AmDREB3 improved the tolerance of transgenic Arabidopsis to drought, high salinity and heat, likely by inducing the expression of certain stress-inducible genes. The transgenic Arabidopsis seedlings also exhibited an obvious purple coloration and significant increases in anthocyanin accumulation and/or oxidative stress tolerance under drought, salt, and heat stresses. These results suggest that the AmDREB3 TF may be an important positive regulator of both stress tolerance and anthocyanin accumulation.