Gene transfer technology changes some of the characteristics of crops. However, genetically modified foods have been reported to have an impact on human health. We proposed a cost effective and highly sensitive biosensor electrode with self-assembled monolayer of gold nanoparticle on a micro hemisphere array to detect genetically modified soybean. An ordered array of micro hemispherical features was formed on a 6-inch reclaimed silicon wafer using photolithography. Then, a thin gold layer was sputtered onto the hemispheres. The wafer was then immersed into a 5 mM ethanol solution of 1,6-hexanedithiol (1,6-HDT) to enable the attachment of one thio-end of 1,6-HDT to the thin gold layer. Next, a colloidal gold (15 nm) solution was dripped onto the wafer and baked on a hot plate in such a way that the monolayer of gold nanoparticles could self-assemble on the 1,6-HDT surface. Finally, we used electrochemical impedance spectroscopy (EIS) analysis to detect genetically modified soybean. Experimental results demonstrate that our biosensor can successfully distinguish the genetically modified soybeans from the normal ones.