To compare the effects of nanometer-sized silver ions and support materials (nano-silver coating material, NM-silver) and silver ions, we exposed zebrafish embryos to both types of nano-silver ions and compared the acute responses during embryogenesis . The amount of silver in the NM-silver (117.16%) was greater than that in the silver ion (4.56%). Both of these materials have different atomic compositions. The silver ion-exposed groups (110 and 20 ppt) showed lower survival rates than the NM-silver-exposed groups (110 and 20 ppt). NM-silver penetrated the skin and blood tube of zebrafish larvae as aggregated particles, whereas, silver ions penetrated the organelles, nucleus and yolk in a spread-out pattern. Microarray analysis of RNA from zebrafish larvae (72 hours post-fertilization) that were treated with either NM-silver or silver ions, showed alteration in expression of the BMP, activin, TGF-beta, and GSK3 beta genes pathway. Additionally, GSK3 beta gene pathway for apoptosis that was related with left-right asymmetry. Gene expression changes in the NM-silver or silver ion-streated zebrafish embryo led to phenotypic changes in the hatched larvae, reflecting increased apoptosis and incomplete formation of an axis.