Seafood is one of the delights of Turkish cuisine, even though it is fairly expensive. If you are allergic to fish or seafood, however, you may still be able to enjoy Turkish cuisine in safety.
Fish is one of the glories of dining in Istanbul and indeed anywhere along Turkey's thousands of kilometers of coastline, and fresh or frozen fish are shipped to inland cities as well. Alabalık (trout) are raised in fish farms for the table. Fish is usually served by itself, looking like a fish, rather than as an ingredient in stews, pastries, etc.
Shellfish (shrimp, lobster, mussels, etc.) and other deniz mahsulleri (deh-NEEZ mahh-sool-leh-ree, "sea harvests") are on many seafood restaurant menus in Turkey, even though consumption of shellfish is prohibited by Islamicdietary law. Because of this prohibition, shellfish are unlikely to be included as unknown ingredients in many dishes. The chef may see it as his responsibility to let diners know if shellfish have been included in a meal so that diners who follow Islamic dietary customs may avoid them.
Traditional Turkish dishes do not usually combine seafood and meat ingredients. Meat and vegetable-meat dishes are just that, in my experience. Many simple ready-food (hazır yemek) restaurants do not serve seafood at all, so their soups, stews, pilavs and kebaps should be safe (as well as inexpensive and delicious).
Meze (appetizers) may include seafood, such as taramasalata (fish roe spread), or fresh sardines (sardalya) or fresh anchovies (hamsi) prepared in various ways, or lakerda (salted, pickled tunny), but in my experience the seafood dishes are pretty distinct and thus easily avoided.
The cuisine of the Black Sea region is particularly rich in fresh sardine and anchovy dishes.
Many restaurants serve both meat and fish, but others specialize in one or the other, so anyone subject to fish or seafood allergy may want to avoid seafood restaurants and prefer those specializing in meat or traditional Turkish ready-food dishes.
I cannot say how careful kitchens are about keeping fish and non-fish dishes, pots, pans separate. I'd guess not very careful. Luckily, in many ready-food restaurants the kitchen is right in front of you, and you can often see how the food is prepared. See also Food Allergy Awareness in Turkey.
Some words:
Fish: balık (bah-LUHK)
Lobster: istakoz (eess-tah-KOHZ)
Octopus: ahtapot (ahh-tah-POHT)
Seafood: deniz mahsulleri (deh-NEEZ mahh-sool-leh-ree)
Shrimp: karides (kah-REE-dess)
Squid: kalamar (kah-lah-MAHR)
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