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In the animated movie Monsters Inc. the monsters which populate the universe all look very different despite the fact that they are presented as being the same species (since they can interbreed).
This begs the question, how can a species exist that has thousands of different forms?
Well, through controlled breeding people have managed to isolate certain characteristics in dogs to the point that even though they are the same species they look significantly different.
However they all still have the same basic biology: four legs, same general shape, a single head with two eyes, a nose, a snout, etc. In Monsters Inc the situation differs significantly.
Some monsters are based on lizards, others on insects, or mammals. Not only do they come in various shapes and sizes, they also vary in the number of limbs they have, the powers they demonstrate (invisibility, flight, etc.), and other critical characteristics which typically define a "species".
So I suggest we take a step back and allow all these different creatures to actually be separate species. However, let them be actual animals. Monsters.
And let the intelligent species be parasitic in nature, inhabiting the body of these monsters and forming a society in which each individual wears the body of a monster the same way that we might wear a suit.
Basically, think along the lines of what the alien invaders in "The Host" are.
examples from earth include dogs, which can nearly all interbreed despite radically different shapes sizes and colors (although, this is arguably not "natural" given the human selection pressure). also, snow goose blue and white morphs. you might also consider the radical sexual dimorphism in various species (e.g. birds of paridise). or even radically different stages of some animals (larva, nymph, catarpillar, butterfly)
more generally, appearance is a function of genetics and selection pressure. typically, a species seeks uniformity in appearance since visible deformity is correlated with genetic damage and defects. there are however some parts of the genome where diversity is highly valued. there has been some research to suggest that human females are more attracted to males when their immune system genes do not line up.
perhaps you could invent a world where some sort of predator or pest would attack animals that look similar. then there would be genetic selection pressure to ensure you children did not look like any other animal of your species. this selection pressure would eventually be reflected in mating preferences and accelerate the diversity.
example selection pressures:
You could achieve a reasonable amount of variation by granting your species a high level of phenotypic plasticity. This is where the morphology, behavior, physiology, etc are changed as an individual grows.
These differences are decided by environmental pressures, such as tadpoles gaining more rotund bodies in order to make it more difficult for salamanders to swallow them, or bichirs gaining more robust shoulders, and walking more efficiently, when growing up on most land, as opposed to in water.
If you choose to take this a bit further, you could have a plausible, and in my opinion interesting, result.
It is possible if your species is artificially created. This species would be assembled from the DNA of multiple other species. Each creature has a different combination of DNA donors, but all have the same base line donor.
For an example if your using humans as your base line, then you could breed a human-bear-bird chimera with a human-whale-starfish chimera, to produce a hybrid.
however ever it possible that whatever children the chimera had would not be able to reproduce. (think of mule)
