The impact that zinc oxide nanoparticles (ZnONP) have on plant physiological responses was evaluated by comparing gene expression changes after Arabidopsis thaliana plants were exposed to ZnONP, in comparison with ionic Zn2+ (ZnSO4) and non-treated controls. After treatment with ZnONP (concentration10 μg L−1), ionic Zn2+ (applied as ZnSO4 at a concentration of 19.7 μg/ L −1), expression analyses via RNA sequencing revealed that 369 genes were down regulated and 249 were upregulated (p < [FDR] 0.05, expression difference < 3). The downregulated genes in ZnONP treated seedlings compared to the Zn +2 ion and untreated controls were mainly abiotic stress (oxidative stress, low temperature) and biotic stress such as defense responsive genes based on the gene ontology analysis. The upregulated genes in response to ZnONP treated plants compared to the Zn +2 ion control plants were mainly photosynthesis, light harvesting complex, and hormone responsive genes such as abscisic acid.