There is ambiguity as to the biologic function of the Nox4 NADPH oxidase with evidence that it is both protective and deleterious in the cardiovascular system. The constitutive activity of Nox4 suggests that the reactive oxygen species (ROS) generated do not function primarily as second messengers. Furthermore, regulation of Nox4 activity is mediated primarily by changes in expression levels. Regulation of alternative splicing and functional effects of Nox4 isoforms are not known. We hypothesized that changes in Nox4 isoform expression and subcellular distribution regulate subcellular redox state and specific cellular processes. We found that Nox4 is differentially spliced in atherosclerotic monkey aortic smooth muscle cells (SMC) with an increase in the shorter, non-transmembrane Nox4D and a decrease in the transmembrane form Nox4A. Analysis of the Nox4 3’UTR identified putative binding sites for the microRNAs miR-9 and miR-25 and these miRNAs were elevated in the SMCs isolated from aorta of atherosclerotic monkeys. Similarly, the overexpression of miR-9 or miR-25 in cultured SMCs increased Nox4D expression and decreased Nox4A expression. Using subcellular-targeted HyPer probes, the overexpression of Nox4A increased ROS in the mitochondria, cytosol and nucleus, whereas overexpression of Nox4D predominately showed increased ROS in the nucleus. Changes in Nox4 expression differentially regulate transcriptional activation of the antioxidant response element and expression of HIF-1α. Knockdown of Nox4 decreased NADP+/NADPH and GSSG/2GSH couples while overexpression increased these redox couples. In addition, changes in Nox4 levels resulted in protein-specific changes in thiol oxidation. These data suggest that Nox4 splicing is in part regulated by miR-9 and miR-25 and the dynamic regulation of subcellular redox status by Nox4 isoforms is a mechanism by which the cell integrates information and coordinates complex signaling pathways.