If your horse is branded (hot or freeze brands) then you start with visible identification and if that brand is in the registry's records it will have a recorded owner listed too.
A brand is also a deterrent to horse thieves as long as it is clearly visible of course. The hip or shoulder brand is visible from a distance whereas under the mane is not. However, brands can be "doctored" so are not a completely foolproof means of identification. Lip tattoos are about the easiest to alter and they also fade over time.
Microchips are still somewhat new era especially with regards to horses. Any cat or dog being imported into New Zealand MUST have a microchip implant and many people overseas use the microchips in connection with Lost and Found Registries as a means of finding a cat or dog that has wandered off or been stolen.
Despite the fact that here in New Zealand we have the "readers" to detect and identify microchips they do not seem to be much in use for horses. Microchips have the advantage of being almost undetectable (without a reader), un-removable and they should last a lifetime.
An excellent way of documenting ownership both for registered and unregistered horses is with photographs. Take pictures of your horse from each side and from behind and in front. Take close up photographs of any distinguishing whorls and unique scars. Take measurements for whorls; ie, if there is one on your horse's neck then measure from the base of the ear back to the whorl and write the information on the back of the photograph.
By the way, this is also a good way of documenting ownership of tack but with the close-ups being of distinguishing permanent nicks, sweat marks, and so on.
Now, here is the real trick to claiming and identifying ownership of your horse. Make sure you have some pictures taken with yourself holding the horse and perhaps even pointing to a distinguishing mark. Write the horse's name, registration number, your name and address and the date on the back of the relevant photographs. Order at least two copies of each photograph. Seal these two sets of photographs in two envelopes. Send one set to yourself by registered mail and store the unopened set in your files. Send the second set to your lawyer or to a family member or friend and ask them to keep the unopened envelope in a safe place to be presented at some future point if called upon. Probably a good idea to not tell them what is in the envelope. Just seal the envelope inside another with the foregoing instructions.
That way if the matter ever goes to court it can make quite an impression if the holder of the second set appears in court with the unopened envelope and is able to say they have no idea of what the envelope contains!
The post office date stamp and dated photographs are usually proof enough in a court that you did in fact have a specific horse and/or tack in your possession at this particular time. This along with the registry's information of the recorded owner should go a long way towards proving the horse is yours.
If you ever find yourself in a situation where someone has your horse and is keeping it against your will, make sure you contact the registry and advise them of the problem. Similarly if you are buying a horse, make sure you receive the correctly filled in and signed Transfer of Ownership papers at the same time as money changes hands.