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The extension of English rule into county Clare in the second half of the sixteenth century resulted in the O’Briens losing much of their political power. O’Brien surrendered his ancient freedoms and recognised the authority of the king of England. Bearing the newly conferred title of earl of Thomond, O’Brien no longer arbitrated in disputes at Clonroad in the traditional manner. Injured parties now pleaded their cases under English law at the assize courts in Ennis. In 1585 the Composition of Connacht put an end to the collection of the customary tribute and substituted money payments instead. In 1588 the O’Briens abandoned Clonroad and moved to Bunratty.  The extent to which the ancient aonach continued under these circumstances may only be surmised. The fairs, if they continued at all in the disturbed conditions of the 1590s, were shorn of much of their medieval trappings. The ending of Nine Years War in 1603 ushered in a period of peace and stability. Gaelic lords, anxious to protect their interests under English jurisdiction, sought out royal patents on fairs and markets. In the first two decades of the seventeenth century, Donough O’Brien, fourth earl of Thomond obtained patents for fairs at Clarecastle in 1606, Ennis in 1609 and Sixmilebridge in 1618.  The character of the new fairs was completely different from those of former centuries. No longer were cattle exchanged between lord and vassal on the basis of reciprocal obligations of duty and service. The new emphasis was on commercial transactions, where livestock was exchanged for monetary payment.
Rather surprisingly, despite the large number of patents obtained by O’Brien, no licence appears to have been taken out on the fairs of Clonroad. It is difficult to say why this should have been. Many patents were speculative in nature. They were taken out for places where fairs might not necessary exist but where it was hoped in time they would develop. Occasionally patents were also obtained as a precautionary measure to prevent the predatory claims of others. Perhaps Donough O’Brien felt that the Clonroad fairs were so well established that his claim to ownership over them could not by challenged and thus he never sought a patent for the fairs. In any event, no licence governing the fairs of Clonroad was issued until 1775. 
The dates on which fairs were held were carefully chosen. It was important that fair days did not clash and that they were held at a time of the year convenient for the farmer. According to the patents the fair days were as follows: Clarecastle fairs were held on 19th May and 1st November, the Ennis fairs on the Tuesday of Easter week and the 24th August, those of Sixmilebridge on 25th April and 25th November.  The earliest recorded dates for the Clonroad fairs are the 21st July  and 3rd October.  These dates no longer reflected the medieval rent days but rather the commercial requirements of the 17th century where young cattle were purchased at the spring and summer fairs and the fattened cattle sold for slaughter at the late autumn or winter fairs. Apart from the right to hold a fair, the patent also conferred on the patentee the right to levy tolls and establish a court of law called a court of Pie Power. The purpose of the court was to collect debts and settle disputes arising at fairs. Toll was levied only on the cattle that had been sold. It was usually levied as the sellers left the fair. Disputes often arose over the level of toll charges. The Earl of Thomond did not run these fairs himself but rather leased them out to the local individuals who ran them on his behalf. In times of peace, between the fees collected by the court and the tolls levied on cattle, leaseholders could make a tidy profit from fairs.
During the Confederate Wars of the 1640s the earl of Thomond fled Ireland and took up permanent residence in England. When peace returned in the 1650s Thomond set the lands of Clonroad to John Gore, a Cromwellian army officer. Gore took up residence in the old castle of Clonroad. In 1658 Thomond leased to Gore the fairs and customs of Clonroad for 21 years.  This is the first indication we have that the fairs continued in operation in the post Cromwellian period. In a renewal of his lease in 1676 Gore obtained from Thomond, not just the fairs of Clonroad, but also a lease of the fairs of Ennis, Clare and Sixmilebridge, for rent of £20 per annum.  Gore in turn sublet the collection of the tolls to various individuals. In an interesting case brought before the manor court of Clonroad in 1684, the toll gatherer, James Moriarty Fitzdonogh, was fined for exacting excessive tolls at the October fair. Fitzdonogh had levied a toll or three pence per yearling bullock on the cattle of Joseph Griffith, when he should only have levied two pence per bullock. The transaction was for the sale of 36 cattle so that Fitzdonogh had obtained three shillings more than his due. 
In the renewal of Gore’s lease with the earl of Thomond in 1676, an important exemption clause was inserted in the agreement. It stated that if war hindered the receipt of profits from fairs no rent was to be paid during such war or troubles. This condition was to prove prophetic on account of the outbreak of hostilities thirteen years later between the followers of James II and William of Orange. While the war lasted, Gore was unable to collect livestock tolls and had subsequently to be exempted from the payment of rent for the years 1689-91. 
We can observe the state of development of Clonroad and the activities carried on there in 1703, when Thomas Moland visited the place as part of his work in surveying the Thomond estate. Moland reported:
Moland’s observations on the fairs of Clarecastle are also of interest. He comments ‘two fairs are held here yearly the best in the county in peaceable times, worth £10 or £12 each fair per annum’.  Clearly the disruption caused by the Williamite wars 1689-91, was still being felt in the early years of the eighteenth century.