The strategic importance of these islands ensured that they attracted the attentions of both National and English forces during the major upheavals caused by the 1641 Rebellion. During this time Inishbofin became a pivotal stronghold in the West and was the last to fall.

Royalist forces held out here with French aid from the Duke of Lorraine and made a last ditch campaign of resistance. After some initial success, which included retaking the Aran Islands, the resistance finally crumbled and the islands surrendered in somewhat controversial circumstances. The Cromwellian regime built the imposing and wonderfully intact Star-Shaped artillery fort at the mouth of the harbour, circa 1656. It is known locally as Cromwell’s Barracks and Don Bosco’s fort. The latter is reputed to have been a Spanish pirate and ally of Graine Uaile. Together the pair kept out intruders from the harbour.  Being raiders, they could also use the same technique to trap merchandised ships in the harbour and avail of their treasures for themselves. To the east lies an impressive cresentic shaped medieval harbour, which still stands over 3m in height at low tide.

With the Cromwellian occupation the islands entered a new and somewhat bizarre stage. The Fort was used as a penal holding for Catholic priests and many remained until the restoration of Charles 11. During the Jacobite wars the fort was again in Irish hands and held out until after the battle of Aughrim in 1691, when they surrendered on good terms to the Williamite forces.

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