On May 18, 1682, William Craven, 1st Baron Craven, Palatine, appointed Joseph Morton as the next Governor of Charles Town.

In 1682, the Lords Proprietors ordered that the southern part of the Carolina province should be divided into three counties: Berkeley, Colleton, and Craven. Berkeley county should embrace Charlestown and extend from Sewee bay on the north to Stono creek on the south. Colleton County was located to the south of this and Craven County to the north.

Though Colleton County was intended to include the Scots settlement at Port Royal, not until near the close of the colonial period were steps taken to organize local government for any of the counties except Berkeley. Those, we shall see, were extremely imperfect.

Until 1683, elections for the Commons House of Assembly were held exclusively at Charles Town, freeholders coming thither from all the settlements to vote, or sending their proxies. This was now becoming a great hardship or an impossibility. An order was therefore issued that votes in the election of 1683 should be polled, not only at Charles Town, but at New London [later Willtown, now gone] in Colleton County. In order to avoid attempts to vote in both counties, they also ordered that voting at the two localities should occur on the same day. Ten members should be chosen from each of the new counties.

Governor Joseph Morton and the Executive Council showed their sympathy with the settlement on Ashley River by disregarding the instruction and holding the election as usual. The Commons House of Assembly thus chosen passed several Acts, among them being one for the protection of the colonists against prosecution for debts contracted out of the colony. This, as well as the conduct of the governor and Executive Council concerning the election, greatly offended the Lords Proprietors, and they ordered that the Commons House of Assembly should be dissolved and no other chosen except in compliance with their instructions. Governor Joseph Morton was removed from office, and a successor for him was diligently sought.

Sir Richard Kyrle, a knight of Ireland, was appointed, but died six months after his arrival in America. Robert Quarry, afterward prominent in the admiralty and customs service, was elected to the office by the Executive Council, and discharged its duties for a brief time, though without appointment from the Lords Proprietors. Quarry, however, was soon charged with harboring pirates, and in September of 1685, Joseph West entered upon a brief third term as Acting Governor. He became involved in the controversy over the payment of quitrents, to which reference has been made in another connection. To him the Lords Proprietors repeated their orders, that the revised Fundamental Constitutions of 1682 should be subscribed and put into force. Realizing that the task imposed upon him was hopeless, Acting Governor Joseph West very soon resigned the office and left the colony not long thereafter.

Landgrave Joseph Morton was now restored to office, and called the Commons House of Assembly together in November of 1685. In obedience to instructions he required its members to subscribe the Fundamental Constitutions of 1682. Twelve of the nineteen representatives refused to do so, on the plea that they had already subscribed those of 1669. Thereupon Governor Morton expelled them from the Assembly. The remaining seven, with the Deputies, transacted the business of the session. But these measures were to no purpose. It was again found impossible to procure the acceptance of the Fundamental Constitutions by the colonists, and Governor Morton in his turn had to give way to James Colleton, a brother of one of the Lords Proprietors.

In the summer of 1686, a Spanish force from St. Augustine made an ascent upon the coast, plundering the country about the Edisto River and destroying Stuart Town, the settlement of the Scots at Port Royal. The colonists at Charles Town and vicinity, forgetting for the time their domestic quarrels and their disputes with the Lords Proprietors, under the lead of Governor Morton began fitting out an expedition of reprisal against St. Augustine. They were absorbed in this task when James Colleton arrived and assumed the governorship.

"However, had Sir Nathaniel Johnson stopped here, many reasons might have been urged in his vindication; but he had other measures in view, much more unpopular and oppressive. He looked upon Dissenters of every denomination as enemies to the constitutions of both church and state, and therefore, to subvert their power and influence, or compel them to uniformity of sentiment, another bill was brought into the assembly, framed in such a manner as to exclude them entirely from the Commons House of Assembly.

"This bill required every man who should hereafter be chosen a member of Assembly, to take the oaths and subscribe the declaration appointed by it, to conform to the religion and worship of the Church of England [Anglican], and to receive the sacrament of our Lord's Supper, according to the rites and usage of that church; a qualification which Dissenters considered as having a manifest tendency to rob them of all their civil rights or religious liberties.

"To carry this bill through the House, all the art and influence of the governor and his party were requisite. In the lower house it passed by a majority of one vote, and in the upper house Landgrave Joseph Morton was refused liberty to enter his protest against it. At this juncture no bill could have been framed more inconsistent with the rights and privileges of the freemen, and more pernicious to the interest and prosperity of the country.

"Dissenters, who were a numerous and powerful body of the people, were highly offended, and raised a great outcry against it. Seeing themselves reduced to the necessity of receiving laws from men whose principles of civil and ecclesiastical government they abhorred, and subjected to greater hardships than they suffered in England, many had formed resolutions of abandoning the colony.

"Loud clamors were not only heard without doors, but jealousies and discontent filled the hearts of many within them, not of Dissenters only, but also of those who adhered to the church." [Alexander Hewat, with minor edits]

As a continuing member of the Executive Council, Joseph Morton voted against the establishment of a state church in the province. He was a commissioner of the provincial library in Charles Town in 1700, and in 1710 was appointed a commissioner "for founding and erecting a free school for the use of the inhabitants of South Carolina." He married the widow, Elizabeth Blake, and they had a son and a daughter. He died in September of 1721.

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