Curiosity bit me.

In the context of human identification, we've used a variety of methods. Mugshots, Bertillon's portrait parle, fingerprints, dentition, et cetera. More recently, DNA has come to the forefront.

Question: if we postulate a Royal Equestrian Constabulary ("REC" in my headcanon - for a parallel, consider a hybrid of the Royal Canadian Mounted Police for Equestria as a whole, with perhaps direct responsibility for Canterlot, as the London Metropolitan Police Service), how do they keep track of their bad actors? I did a hasty Google search, and this seems to be fairly definitive human state-of-the-art.

I considered cutie marks as a variation on freeze-branding or recording of hair patterns [op cit.], but, if we have only cartoon-level rendering, it wouldn't necessarily eliminate the close non-matches from what we've seen. OTOH, we can reasonably expect that an actual pony world, things would operate at a much higher resolution... Nose prints from dogs have been demonstrated to be readily individualized, but that doesn't seem to hold true for horses, owing to different skin structure. I recalled a passage from one of Fleming's James Bond novels where he asserted that chestnuts were as readily identifiable as fingerprints, but this seems to be a bit overstated, given the other articles I read when I searched the topic.

What do you guys think?

Ponies do a lot of manipulating objects with their mouths. You rightly brought up dentition as a means of identifying individuals, and that should extend to most creatures that have teeth (or a beak) because the wear patterns will always be unique. It’s not just used in criminal forensics, but in every field science that deals with living or dead critters. Horses do experience continual tooth growth and wear, so an exact print wouldn’t match perfectly after a few years, but there are other aspects like the horse’s age that can be determined.

One fantastic thing about teeth is that they’re far and above the most reliable way to identify minute variations in species amongst animal and fossil skeletons, as even small evolutionary niche differences will show up in the development of the teeth in an identifiable fashion that’s easy to compare. It’s easy to imagine that a skilled pony investigator could tell if a set of choppers belonged to a Pegasus or a Earth Pony right off the bat without consulting a database.

Even if ponies are dexterous enough to not leave indentations on every object they pick up, they may leave “biteprints” with their dried saliva the way we leave fingerprints with the oils on our hands. Not sure if those would have the same staying power hours or days later, because saliva is weird. Anybody on the biology side who can confirm?

Unicorns use magic a bit more often than their mouths, so this is something tied to how magic works in your headcanon. Some fantasy settings (and several ponyfics I can think of) treat magic as having a “signature” unique to the spellcaster. Spells may leave behind a trace after the unicorn is no longer present, and if you want to you can introduce all sorts of unique kinds of problems for the investigators who deal with magical crimes. Maybe magic leaves a signature, but it can’t be physically recorded so they can’t store the evidence to use it in court or keep it in a database. Suppose that a nearby alchemist’s laboratory is totally throwing them off by flooding the area with ambient magic which makes it hard for them to get a good reading? Or perhaps a powerful changeling can “forge” a magical signature. Lot of possibilities.

I don’t have much knowledge on identification of individual non-fossil horses, sadly. Somebody else might be able to help there.

The first thing that cam to mind when you mentionned mouth manipulations is trace of saliva.

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Having done some experimentation, I can say that you don't get as much saliva on a book when you hold it in your mouth as you'd think. It's going to depend on how you hold it, of course. Likewise, tooth impressions are limited--in a paperback copy of Birds of Michigan, I left two canine imprints on the front cover by the spine, and 2 caninies + 1 incisor on the back cover. Obviously, there would be a lot of variability (how long it was held, how forcefully it was held, etc.). So I guess I'd say that it isn't utterly dependable--a pony detective might or might not get any dentition for analysis.

If they did, I can imagine a few things being helpful. Whether or not the pony in question has canine teeth or wolf teeth, for example. How recently they were filed--there might even be signatures that some dentists have (i.e., maybe Colgate likes to round the edges a little bit, whereas some other dental pony prefers a more straight filing).

Lip prints might be a thing. I don't know how unique they are in equines (or humans, for that matter), but even if they can't positively identify, they can likely eliminate suspects.

Hoofprints could be a big deal. Shoes, if worn, would likely have a distinctive pattern both of nails and of wear to the shoe itself, as well as type and size. That could quickly narrow down a list of suspects--if they're foal-sized shoes, you can probably rule out Big Mac as the culprit.

There's a possibility that frogs are somewhat unique in shape--that could be another helpful clue when it comes to hoofprints. Other stuff like stride might help identify or eliminate suspects, or other types of gait issues (a lame leg, for example).

I'm sure that Uncle Mike came across the mention of horses having eight blood groups (A, C, D, K, P, Q, U, and T), which if the ponies can type blood at all might also be a useful test.

Obviously, the large variations in coat color and mane color could be helpful for a detective. Seeing a literal rainbow of tail hairs at a scene would suggest either multiple criminals or just Rainbow Dash, for example.

Pegasus feathers could potentially leave a pattern (in blood or dust, for example), and that could also be an identifier.

Likewise, unicorn horns might all be unique, although it's hard to think of a circumstance where a unicorn would leave an impression of her horn at a crime scene.

Going further down the rabbit hole, I don't think that ponies have very good microbiology, so things like DNA tests are probably out (at least from a purely scientific standard).* They might be able to do some old-fashioned blood typing (serum tests, for example). There could be blood types that are more or less common among different tribes of ponies, or there could be some combinations that could only occur in half-breeds (for lack of a better term)--for example, the Cake Twins might have a blood type that's rare or impossible for pureblood unicorns or pegasi.
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*In a MLP-'verse where they do have DNA tests, it's hard to imagine that you wouldn't be able to find DNA on things that had been manipulated by earth ponies or pegasi, unless the perpetrator wore a dental dam of some sort.

There could be spells that enchant hair to find its kin, and that hair might react when the pony who shed it was nearby. Although I'm not terribly fond of that solution, since it implies that a unicorn could fake the test and make the hair wiggle on command, and at least for the sake of plotting out a detective story, why not go whole hog and have there be truth-telling spells? [Granted, that could be the entire point of the story, so it's not undoable (and in fact, that subject comes up in OPP).]

I think that magic does leave some kind of signature behind, but that its intensity is proportional to what was done, and could also potentially depend on the precision that the unicorn casting the spell had. In general, I'd think that Rarity lifting a spool of thread would leave behind much less of a signature than Twilight lifting a water tower. Particular spells might only be known by a few unicorns, or might be beyond the ability of a particular unicorn to cast.

Thinking of that, the color of the corona varies between unicorns, and while that might not be a positive identifier, it could also eliminate suspects. If the aura's blue-green, it wasn't Lyra that cast that spell.

In terms of cutie marks, I think that they are unique, at least upon close inspection. I think that ponies often use them as identifiers, rather than writing out whole names--kind of like heraldry. I don't think that they can be changed without magic (Starlight's spell) or else coat paint (Starlight's personal technique). I'd think that any worthwhile pony detective would be able to figure out if the mark had been changed by magic . . . or was just painted on.

I've read some non-pony stories where various types of magical brands are used to mark criminals, and it's possible that ponies could do that. Tampering with such a mark might be illegal, and since the ponies are big on redemption they would probably take it off after time was served. Maybe not, though. Maybe that's why Fluttershy nearly always has her mane covering her neck.

I should also mention with freeze branding, since it just takes the pigment out of the in most cases, ponies have probably invented fur dye and a good stylist is probably very skilled at matching natural fur color. As with the cutie marks, that wouldn't pass close inspection, but from a distance it would render the brand invisible.