Based on previous studies and preliminary test results, 200 μM was used as the test concentration of chromium (Cr), and changes in the gene expression profile of Arabidopsis thaliana in response to 24-h treatments of Cr(III) and Cr(VI) were analyzed using the Arabidopsis ATH1 Genome Array. The results were as follows. There were 238 upregulated genes and 858 downregulated genes in response to treatments with Cr(III) and Cr(VI). For Cr(III) and Cr(VI) treatments, there were 185 and 587 specifically upregulated genes as well as 220 and 956 specifically downregulated genes, respectively. Among the common differentially expressed genes (DEGs), the expression levels of genes involved in redox, secondary metabolism, and energy metabolism processes were significantly downregulated, while those of genes related to the stress response, photosynthesis, and sulfur metabolism were significantly upregulated. These findings indicated that Cr seriously affected the normal activities of A. thaliana cells. Some genes associated with stress and regulation were upregulated to adapt to the stress caused by Cr. Among the unique DEGs, the expression levels of genes involved in indole-3-acetic acid (IAA) regulatory pathway were significantly increased in response to Cr(III) treatment; the expression levels of genes involved in the abscisic acid (ABA) regulation pathway and carotenoid synthesis were significantly increased following Cr(VI) treatment. These results revealed some differences in response to Cr(III) and Cr(VI) in A. thaliana.