This article examines the influence of a distinct Irish Protestant faction on parliamentarian policy-making in the mid-1640s – the Irish Independents. These men were not merely clients of parliament’s lord lieutenant, Viscount Lisle, but formed a group with consistent personnel and policies, which can be traced back to the ‘Boyle group’ in the Irish council of the 1620s and 1630s. In the 1640s they came into an alliance with the English Independents, based on common hostility to the Presbyterian party, the Scots, and the supporters of Ormond and Inchiquin in Ireland. This coalition was, however, inherently unstable. Faced with equivocation at Westminster, where Ireland had always been low on the list of priorities, from December 1646 the Irish Independents were forced to take charge of parliament’s Irish policy, and many of the initiatives previously attributed to Lisle in 1646–7 can more properly be laid at their door. In conclusion, it is suggested that the Irish Independents represent a radical strain in Irish Protestantism, which supported Ireland’s closer integration into an ‘English Empire’, and which would see its fulfilment in the unionist agenda developed in the 1650s.