Every horse, donkey and pony in England and Wales is now required to have its own passport.
Horse-lovers support the move
The regulations come in response to a European directive aimed at preventing horses treated with certain drugs from being sold as horsemeat.
The documents will identify each individual horse and show a record of which medicines the animal has taken.
The passports cost around £20 each but owners face fines of up to £5,000 if they fail to comply with the new rules.
Animals without a passport cannot be sold or exported, moved from one place to another or slaughtered for human consumption.
BBC environment correspondent Richard Black says horsemeat is not a major concern in the UK, but horse-lovers generally support the move.
It is hoped theft of animals will become more difficult.
Northern Ireland introduced similar regulations in January and Scotland is due to follow suit.
The total number of horses and ponies in Great Britain is estimated at between 600,000 and just under 1m.