I am trying to identify a short story I read years ago in an anthology.
You may be slightly misremembering Jack Vance's novelette "The Narrow Land", which was also the answer to the question Short story about amphibious species. In Vance's story the variable is the number of crests, not eyes. First published in Fantastic, July 1967 (available at the Internet Archive), it has appeared in some Vance collections such as The Narrow Land and Green Magic and (in French as "La terre étroite") Docteur Bizarre. Do any of these covers look familiar?
From what I remember, it dealt with frog like creatures.
Others inhabited the water; Ern saw their dim shapes to all sides. Some were like himself: pale pop-eyed sprats, narrow-skulled with wisps of film for crests. Others were larger, with the legs and arms definitely articulated, the crests stiffer, the skin tough and silver-gray. Ern bestirred himself, tested his arms and legs. He swam, carefully at first, then with competence. Hunger came; he ate: larvae, nodules on the roots of reeds, trifles of this and that.
They are naturally born one-eyed but the breeding process can be manipulated for them to have two eyes and be sentient instead.
They are all sentient, but the two-crested neuters are more intellectual:
The larger of the water-children tended to congregate at the surface. There were two sorts. The typical individual was slender and lithe, with a narrow bony skull, a single crest, protuberant eyes. His temperament was mercurial; he tended to undignified wrangling and sudden brisk fights which were over almost as soon as they started. The sex differences were definite: some were male, half as many were female.
In contrast, and much in the minority, were the twin-crested water-children. These were more massive, with broader skulls, less prominent eyes and a more sedate disposition. Their sexual differentiation was not obvious, and they regarded the antics of the single-crested children with disapproval.
Ern identified himself with this latter group though his crest development was not yet definite, and, if anything, he was even broader and more stocky than the others. Sexually he was slow in developing, but he seemed definitely masculine.
The protagonist has to hide that he has three eyes and tries to create more creatures like him. In the last sentence, it is revealed that a monster that he had to flee as a child has four eyes.
He is trying to create more "Threes", i.e., three-crested individuals, formed by the fusion of three eggs. A quotation from near the end:
Once more in the hall Mazar arranged the eggs on a stone settle. He made a sound of satisfaction. "In each clutch are two round eggs and one oval: male and female; and we need not guess at the combinations." He reflected a moment. "Two males and a female produce the masculine Three; two females and a male should exert an equal influence in the opposite direction . . . There will necessarily be an excess of male eggs. They will yield two masculine Threes; possibly more, if three male eggs are able to fuse." He made a thoughtful sound. "It is a temptation to attempt the fusion of four eggs."
"In this case I would urge caution," suggested Ern.
Mazar drew back in surprise and displeasure. "Is your wisdom so much more profound than mine?"
Ern made a polite gesture of self-effacement, one of the graces learned at the Two school. "I was born in the shallows, among the water-babies. Our great enemy was the ogre who lived in a slough. When I searched for eggs, I saw him again. He is larger than you and I together; his limbs are gross; his head is malformed and hung over with red wattles. Upon his head stand four crests."
Mazar was silent. He said at last: "We are Threes. Best that we produce other Threes. Well then, to work."
The last paragraph:
"There will be two females," declared Mazar. "Of this I am certain. I am old—but, well, we shall see."