Fish are permissible for consumption when they bear the two kosher signs the Torah lists, which are fins and scales. The Poskim discuss whether fish that have scales which are only visible under a microscope are kosher because they in fact do have scales or if they are considered non-kosher because these scales cannot be seen by the naked eye.
This question of whether or not something seen under a microscope is taken into consideration or not has many ramifications. For instance, Halacha dictates that if an animal’s lung is punctured, the animal is considered a “Terefa” and is forbidden for consumption. The discussion becomes whether or not a hole in the animal’s lung which cannot be seen by the naked eye but is clearly discernible under a microscope is considered grounds for deeming the animal non-kosher and forbidden for consumption.
Hagaon Harav Chalfon Moshe Ha’Kohen zt”l (head of the rabbinical court in Djerba, Tunisia approximately sixty years ago whose bones were recently brought to Israel for reburial) writes that fish whose scales can only be seen under a microscope are not permissible at all, for the Torah only permits or prohibits things that are able to be seen by an individual with healthy eye-sight. For this reason, the Torah only forbids punctures or holes in an animal’s organs that can be seen by man’s naked eye and not through any external instrument. He concludes by saying, “My grandfather, Hagaon Harav Moshe Ha’Kohen zt”l, ruled likewise on a similar matter brought before him: Water that was strained and filtered many times was brought before him and even so, when looking at the water under a microscope, many worms and creatures were visible crawling in the water. He replied that the Torah only prohibits worms which are visible with one’s natural eye-sight.” Similarly, the Aruch Ha’Shulchan writes that although there are many creatures visible in water under a microscope, the water is permitted for drinking, for the Torah only prohibits what the human eye can see unassisted since the Torah was not given to angels. If this were not the case, many researchers write that the air is full of tiny, microscopic organisms and when one opens his mouth, he swallows some and nevertheless, no one would even contemplate for a moment that breathing is prohibited as well! It must be that anything which is unable to be seen by the naked eye is not taken into consideration. Nevertheless, anything which is visible to the human eye, even if must be held to the sun or if it is extremely small (such as regarding vegetable leaves and the like) is absolutely considered an insect and is prohibited for consumption.
Based on this, fish whose scales are only visible under a microscope are forbidden for consumption. On the other hand, water which contains tiny organisms or worms visible only under a microscope is permissible for drinking. Similarly, fruits or vegetables containing worms only visible when checked under a microscope are permissible for consumption. However, if the worms or insects are detected by a microscope but are afterwards discernible with the naked eye as well, they are forbidden for consumption. Thus, a microscope or any other magnifying instrument may be used to ease the process of checking vegetables for worms or insects; after they are checked with the microscope, one should check to see if the insects are visible with the naked eye, for if they are, they are prohibited and if they are not, there is indeed room for leniency.