Objective: A comparative study was performed in order to identify aqueous humor amino acids possibly involved in cataract formation in farmed Atlantic salmon. Methods: Aqueous humor amino acids from farmed salmons with and without cataract were compared with levels in wild salmon and other animals of different evolutionary levels such as frog, crocodile, turkey, goose, minke whale, and cattle. Serum samples from wild and farmed salmon and minke whale were also analyzed. Results: The total amino acid concentration was lower in aqueous humor obtained from salmon, frog and crocodile compared to birds and mammals. Wild salmon had a higher content of amino acids than farmed salmon. Asparagine was absent in salmon aqueous humor and serum. Aqueous humor proline was readily detectable in wild salmon, birds, whale, and cattle, but not detectable in farmed salmon, frog and crocodile. The aqueous humor concentration of taurine was about seven- and fifty-fold lower compared to serum in wild and farmed salmon, respectively. The corresponding ratio in minke whale was 1:2. Conclusions: The results indicate a blood- aqueous barrier for taurine in farmed salmon. The lower total amino acid concentration and low aqueous humor proline concentration in farmed salmon should be further investigated.