Plants possess a well-organized protective network, wherein antioxidant enzymes play an important part in dealing with oxidative stress induced by over accumulation of ROS in plant cells. In the present study, a microcosm hydroponic experiment was performed to investigate the molecular modification of antioxidant enzymes at subcellular levels in rice seedlings in the presence of either trivalent Cr(III) or hexavalent chromium Cr(VI) using rice oligonucleotide microarray analysis. The results indicated that the production of ROS induced by Cr(III, VI) was concentration-dependent, Cr-specific and tissue-specific. Trivalent or hexavalent chromium exposure significantly (p < 0.05) altered the antioxidant enzymes activities in both rice tissues in comparison to control plants. In total, 41 genes were identified from the data of rice oligonucleotide microarray analysis. Under Cr(III) exposure, relatively higher expression of genes was observed in roots compared to those in shoots (p < 0.05), while gene expressions in both plant parts differed slightly during Cr(VI) exposure, implying different regulation and response strategies of plants against Cr(III) and Cr(VI). Subcellular localization indicated that genes encoding SOD, POD, APX, and GPX are mainly prevalent in the cytoplasm (30.77%), chloroplasts (29.23%), peroxisomes (10.77%) and mitochondria (9.23%), suggesting that cytoplasm and chloroplasts are the main sites responsible for scavenging ROS through enzymatic processes. Our study provides new insight into the roles of antioxidant enzymes in ROS metabolism at subcellular levels under Cr exposure. Display omitted •Generation of ROS induced by Cr was concentration-dependent and tissue-specific.•Cr exposure altered the activities of antioxidant enzymes in both roots and shoots of rice plants.•41 antioxidant enzymatic genes corresponding to Cr were identified by microarray analysis.•A gene regulation diagram of eight antioxidant enzymes at the subcellular levels is proposed.•Genes encoding antioxidant enzymes are predominant in the cytoplasm and chloroplast.