They are concepts given living, physical form. Each pokemon usually encompasses at least two ideas (some many more), combined into a single creature that best represents the whole.
Take Ludicolo, a pokemon with many ideas behind it: “duck”, “Japanese raincoat”, “lily pad”, “pineapple”, “Mexican dancer”, “kappa”. It takes aspects of all of these ideas and becomes something new.
The bigger question is: do the concepts they’re based on come from the collective unconscious of mankind? Other pokemon? All living things? A creator god?