I used to go to JAX about every month for work, and always stayed near the beach. Dolphin Depot was one of my favorite places to eat, but I hear that it's slipped.
I also enjoy The Homestead and Aqua Grill. I'm headed to JAX this weekend and am wondering which of the three is still good (I haven't been there in about 2 years).
I am also open to new suggestions if any new places opened. I'd prefer to stay near the beach, though I will make an exception for BB's. :)
It's not seafood, but right down the street from the Homestead, you'll find Mojo's Kitchen, which has a full bar, outstanding BBQ (all styles - Todd, the owner is a carolina boy who not only has good pulled pork, etc. but makes a darned fine brisket.) I recommend the onion rings (best in town) and the smoked corn - they cut it off the cob, smoke it in pans in the smoker, and add a lil butter 'n salt. Addictive. A source for Cheerwine, for those who know. Often there will be live music - if you like blues, it's a good stop.
here's a link:
Ocean 60 on 1st street just north of Atlantic Blvd has very good seafood, though it is noisy. The hotel across 1st street just finished a complete remodeling and there is a new restaurant in it that just opened (5/23). We haven't tried it but the view will be spectacular. Our beach favorite is 11 South which is on 11th Avenue South in Jacksonville Beach, just to the east of A1A (third st.) There is also Roys (Hawaiin fusion) farther south on A1A just over the border into Ponte Vedra Beach; very good but somewhat pricey. It's on the west side of A1A in a shopping center. A bit farther south in the same shopping center has a Bonefish Grill which is reliably good.