What is the rarest sea creature you have ever seen?

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It depends on whether you mean rarest animal anywhere or rarest in a specific geographic region. I saw the first whitetailed damsel in California waters although it isn't rare further south.

I wouldn't consider the giant sea bass mentioned earlier as a rare species. Their SoCal population was decimated by over fishing years ago, but I've been filming them for nearly 20 years and have seen as many as several dozen at once.
Ian Uhalt recorded this off Palos Verdes a couple of years ago.

Bill Macdonald shot this at the Star of Scotland wreck off Santa Monica.
 
I saw an electric ray called an Atlantic Torpedo on a shore dive off Cape Anne Massachusetts.
 
Saw it twice at LBTS.

If the criteria is "something I saw only once at a place I dived many times", then I can name the following

1. Naked sole at BHB
2. Giant boxcrab in Hawaii
3. Bluespotted cornetfish in Curasao
4. Spanish dancer in bright daylight in Hawaii
5. Hawaiian longfin anthias
6. Hawaiian green lionfish
 
Not a sea-creature, but, a small group of otters in Lake Jocassee SC. Almost as supple as water, for lack of a better description....
 
As Bill says it depends on definition of rare. I have had a couple of sightings diving off NC that had not previously been reported in the REEF database for NC. But they were very common down toward the Keys. Yellow tail snapper is one.
 
Baby Scorpion fish about an inch long. It was hardly noticeable with the small coral chunks surrounding it. One of my students was doing a fin pivot and she noticed something move, just slightly, when her face got close to the bottom. She kept moving her arm (she was pointing) and I kept trying to encourage her to stop moving. And then, the baby scorpion fish flared its fins. They were brightly colored, yet small. If only I had a camera.
 
A Helmet Gunard at Barnegat Light, NJ, a Blue Tang at Martha's Vineyard, Mass., a yearling Leatherback Sea Turtle, shell about 16 inches, in Negril, Jamaica, a juvenile (about 8 inches) Oceanic Sunfish in Dominica.
 
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