Multiwall carbon nanotubes (MWCNTs) have many attractive properties with potential applications in various fields. Despite their usefulness, however, the associated waste can be hazardous to the environment. To examine adverse effects in aquatic environments, Oryzias latipes were exposed to MWCNTs dispersed in water for 14 days and apoptosis and antioxidant gene expression were observed. This work showed that in gills exposed to 100 mg/L MWCNTs for 4 days, there was significant p53, caspase-3 (Cas3), caspase-8 (Cas8), and caspase-9 (Cas9) gene expression relative to the controls, while catalase (CAT) and glutathione-S-transferase (GST) expression were reduced. At 14 days, CAT, GST, and metallothionein (MT) were induced significantly in the gills and Cas3, Cas8, and Cas9 were induced in the liver. No significant gene induction was seen in intestine. Intracellular reactive oxygen species (ROS) were increased significantly only at 14 days. Histologically, no apoptosis was observed with exposure to 100 mg/L MWCNTs for 21 days. The gills were more sensitive to MWCNT toxicity than the other organs. Males had higher apoptosis gene induction than females. These results demonstrated that MWCNTs could cause apoptosis in a manner influenced by tissue and gender in aqueous environments.