the naked eye
Normal vision that has not been enhanced or augmented in any way. Because bacteria are invisible to the naked eye, it was only relatively recently in human history that we even became aware of their existence. The fine print is so tiny, you can barely make it out with the naked eye.
with the naked eye
with eyes that are not aided by telescopes, microscopes, or binoculars. The moon is quite visible with the naked eye. Bacteria are too small to be seen with the naked eye.