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Zoanthus have smaller polyps and reproduce by forming buds from the base of the mated
tissue. The species unlike some of the others in the family does not incorporate sediment into
it’s base. The oral disk is in the center of tightly packed tentacles and appear in nature in a
variety of colors and endless combinations.

Palythoa have larger polyps but are also embedded in a common tissue. The texture of the
base of both the Palythoa and Protopalythoa is rough from the incorporation of sand and
sediment directly in the tissue. The assimilation of the material is thought to be both for
defense and support. The larger polyps lend themselves to feeding on larger meatier foods.

Protopalythoa much like the Palythoa in size but with the exception that the polyps are not
connected to one mass of tissue. Some seem to have less more pointed tentacles in some
cases they even alternate up and down (Sprung 2001)
 
What crazy said!

The physical distinctions between zooanthids and palythoas will lend themselves to be easier seen as you've spent more time trolling the forums. ;)

Zooanthids tend to be more colorful (opinion, but not absolute) with varying patterns. They will tend to form a mat, covering an area of rock like it were grass, whereas palys tend to generate polyps apart from each other and grow to be much larger. Palys get to be pretty big and will catch meaty foods which land in their polyps! It's cool to watch during feeding time. They make an excellent accent to the lower rocks, reaching up from the sand bed to the light.

Palythoas still come in very striking colors, radiant green, electric blues, and so on. Be wary, though, of the substance called "palytoxin." Some palys carry more of this neurotoxin than others, but most of the ones you see will be fine.

Whether you choose to go with zoos, palys, or BOTH, you'll be in for a real treat as far as color and presentation are concerned. :)
 
in simple words, palys are big and they are not attached to each other. Zoas are smaller and bundled together.
 

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