It has now become mandatory to implant a microchip into a dog, but for the dogs you had before this system was put in place, it is not mandatory but recommended.
ご質問ありがとうございます。
"It has now become mandatory to implant a microchip into a dog,"=「今は、犬にマイクロチップをインプラントするのが義務化された。」
"but for the dogs you had before this system was put in place,"=「でも制度が出来る前に飼っていた犬の場合は」
"it is not mandatory but recommended."=「義務ではなく、推奨されている。」
ご参考までに。