The Commonwealth (1649-53) was the political structure during the period from 1649 to 1660 when England and Wales, later along with Ireland and Scotland, were governed as a republic after the end of the Second English Civil War and the trial and execution of Charles I. The republic's existence was declared through "An Act declaring England to be a Commonwealth", adopted by the Rump Parliament on 19 May 1649. Power in the early Commonwealth was vested primarily in the Parliament and a Council of State. During the period, fighting continued, particularly in Ireland and Scotland, between the parliamentary forces and those opposed to them, as part of what is now referred to as the Third English Civil War. (Wikipedia Article).

The Protectorate (1653-59) was the period during the Commonwealth (or, to monarchists, the Interregnum) when England and Wales, Ireland, Scotland, and the English overseas possessions were governed by a Lord Protector as a republic. The Protectorate began in 1653 when, following the dissolution of the Rump Parliament and then Barebone's Parliament, Oliver Cromwell was appointed Lord Protector of the Commonwealth under the terms of the Instrument of Government. In 1659, the Protectorate Parliament was dissolved by the Committee of Safety as Richard Cromwell, who had succeeded his father as Lord Protector, was unable to keep control of the Parliament and the Army. This marked the end of the Protectorate and the start of a second period of rule by the Rump Parliament as the legislature and the Council of State as the executive. (Wikipedia article).

BNJ References for the Commonwealth and Protectorate