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The simple answer to this question would be that magical creatures are capable of using magic as an evolutionary advantage. Magical abilities are often considered to be "wondrous" and "special", but as we know, there are plenty of non-magical animals with unique characteristics like the changing of colours (the chameleon) or biological immortality (Turritopsis dohrnii). In other cases, both magical and non-magical animals share the same ability; for example, the lotus leaf and augurey feathers are able to repel water but only one has a magical origin.

I appreciate that this question can lead to a discussion about how wizards do generally distinguish between "physical" and "magical" phenomena but since wizards don't use scientific methods like non-magical scientists, it strikes me that they would struggle to detect whether a phenomenon is "physical" or "magical" in its nature.

How can they distinguish between creatures that are magical and those that are mundane?

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    They go and buy "Fantastic Beasts and Where to Find Them" and look them up – Valorum Mar 12 '16 at 15:29
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    You'll need to roll a 4 or better – Valorum Mar 12 '16 at 15:37
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    Dumbledore detects magic with a simple touch. I think we can assume that a well trained magiczoologist would have much the same ability, detecting an animal's magic by its mere presence. – Valorum Mar 12 '16 at 15:38
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    There's an app for that. – Peregrine Rook Mar 12 '16 at 16:26
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    @Imaginarrate Probably by doing whatever wizards do to test stuff for magic. I know, for instance, that bears are related to raccoons - but I personally had no way of determining that. Some scientist armed with a microscope and a PhD determined that and put it in a book, and then I looked it up. – Misha R Mar 12 '16 at 18:06
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In the muggle edition of "Fantastic Beasts and Where to Find Them", Newt Scamander offers some fascinating insights into the detection process of magical animals

Dissection (and presumably vivisection)

I look back across the years to the seven-year-old wizard who spent hours in his bedroom dismembering Horklumps

Careful observation

I have visited lairs, burrows, and nests across five continents, observed the curious habits of magical beasts in a hundred countries, witnessed their powers, gained their trust and, on occasion, beaten them off with my travelling kettle.

Attraction to magic

Chizpurfles are small parasites up to a twentieth of an inch high, crablike in appearance, with large fangs. They are attracted by magic and may infest the fur and feathers of such creatures as Crups and Augureys.

The production of magical byproducts

The Glumbumble ... is a grey, furry-bodied flying insect that produces melancholy-inducing treacle, which is used as an antidote to the hysteria produced by eating Alihotsy leaves.

Intentional concealment by the creature

International Confederation of Wizard observers realised that they were not dealing with a true serpent when they saw it turn into an otter on the approach of a team of Muggle investigators and then transform back into a serpent when the coast was clear.

Possession of unusual characteristics that defy muggle logic

The Occamy is aggressive to all who approach it, particularly in defence of its eggs, whose shells are made of the purest, softest silver.

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    It didn't really answer the question.. – I Love You 3000 Mar 31 '17 at 20:29
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    @ILoveYou - Yes it does, especially the latter three. – Valorum Mar 31 '17 at 20:33
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    Lots of muggle creatures become aggressive to protect their eggs. Also, having silver shell doesn't mean the egg is magical. When new things are discovered, we try to explore it, not declare it magical. – I Love You 3000 Mar 31 '17 at 21:16
  • @ILoveYou - In the quote it makes it clear that if an animal uses magic to conceal itself, that's clearly evidence that the creature is magic. By the same token, if the creature's biology defies common (muggle) sense, then it's likely to be a beast. – Valorum Mar 31 '17 at 21:19
  • @Valorum I'd say a lot of non magical animals defies common muggle sense, becoming a mystery for the science (as was stated in the question). That doesn't make them magical. Yet lots of magical creatures in HP universe don't look that much mysterious - what's wrong with hippogrifs or nifflers for instance? What would happen if Muggles find out about hippogriffs? Why they should be kept hidden? – Shana Tar Nov 12 '18 at 8:04

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