Until now, pupils on both sides of the border have sat the same tests. But from next year the tests will solely be devised by the Welsh curriculum body, ACAC.
The move comes as responsibility for education in the principality moves from London to the new National Assembly in Cardiff, formally opened on July 1.
The decision on testing was taken last year by the Welsh Secretary, and the differences had already started to develop.
ACAC chief executive John V Williams said the split was a natural next step, and would mean a more effective system.
The Welsh education system has traditionally been closer to the English system than that of Scotland. But the Institute of Welsh Affairs, which has launched a campaign for a Welsh Baccalaureate to replace A-levels and general national vocational qualifications, said differences were growing.
Recent changes in Welsh tests have included dropping the written Shakespeare test at key stage 3 on ACAC's advice that the teaching of the Bard was secure enough to make it unnecessary. It continues to form part of teacher assessment, which the agency has always rated equally to tests.