Acadian Civil War The Acadian Civil War ( 1640 - 1645 ) was fought between competing governors of the French province of Acadia . Governor Charles de Saint - Étienne de la Tour ( a Protestant ) had been granted one area of territory by King Louis XIV , and Charles de Menou d ' Aulnay ( a Catholic ) had been granted another area . The divisions made by the king were geographically uninformed , and the two territories and their administrative centers overlapped . The conflict was intensified by personal animosity between the two governors , and came to an end when d ' Aulnay successfully expelled la Tour from his holdings . D ' Aulnay ' s success was effectively overturned after his death when la Tour married D ' Aulnay ' s widow in 1653 . Historical context . In 1635 , Governor of Acadia Charles de Menou d ' Aulnay de Charnisay moved settlers from present - day LaHave , Nova Scotia to Port - Royal ( present day Annapolis Royal ) , and the Acadian people began to establish their roots . Under d ' Aulnay , the Acadians built the first dykes in North America and cultivated the reclaimed salt marshes . During this time , Acadia was plunged into what some historians have described as a civil war ; the two main centres were Port - Royal ( present day Annapolis Royal ) , where d ' Aulnay was stationed , and present - day Saint John , New Brunswick , where Charles de Saint - Étienne de la Tour was stationed . The strategic location at the mouth of the St . John River was fortified by Charles de la Tour in 1631 . The fort was named Fort Sainte Marie ( AKA Fort La Tour ) and was located on the east side of the river . To the west of the St . John River , Fort Saint - Jean was later built ( c . 1790 ) . Both La Tour and d ' Aulnay had claims of some legitimacy to the governorship of Acadia because the French Imperial officials made their appointments with an incomplete understanding of the geography of the area . LaTour had a fortified settlement at the mouth of the Saint John River while d ' Aulnay ' s base was at Port Royal some 45 miles across the Bay of Fundy . In adjoining New England , the people supported LaTour ' s claim since he allowed them to fish and lumber in and along the Bay of Fundy without let or hindrance while d ' Aulnay aggressively sought payment for that right . Word came to LaTour that d ' Aulnay was concentrating men and materials for an attack on LaTour ' s fort and fur - trading operation at the mouth of the Saint John River . La Tour went to Boston to ask John Winthrop , the governor of Massachusetts Bay colony , for help . Winthrop arranged for several merchants to advance loans unofficially to La Tour for his purchase of men and material to defend the Saint John River fort from d ' Aulnay ' s attack . War . Battle of Port Royal ( 1640 ) . La Tour arrived from present - day Saint John , and attacked Port - Royal ( Annapolis Royal ) with two armed ships . D ' Aulnay ' s captain was killed and La Tour and his men were taken prisoner . In response to the attack , d ' Aulnay sailed out of Port - Royal to establish a blockade of La Tour ' s fort at present - day Saint John . Blockade of St . John ( 1642 ) . For five months , the Governor of Acadia d ' Aulnay , who was stationed at Port Royal , created a blockade of the river to defeat La Tour at his fort . On 14 July 1643 , La Tour arrived from Boston with four ships and a complement of 270 men to repossess Fort Sainte - Marie . After this victory , La Tour went on to attack d ' Aulnay at Port Royal , Nova Scotia . LaTour was unsuccessful then in catching d ' Aulnay and the rivalry continued for several more years . Battle of Penobscot ( 1643 ) . d ' Aulnay was stationed at Penobscot ( present - day Castine , Maine ) . La Tour attacked in July with 140 men on four ships . Several on both sides were killed in the action . Battle of Port Royal ( 1643 ) . In 1643 , La Tour tried to capture Port - Royal again . La Tour arrived at Saint John from Boston with a fleet a five armed vessels and 270 men and broke the blockade . La Tour then chased d ' Aulnay ' s vessels back across the Bay of Fundy to Port - Royal ( Annapolis Royal ) . D ' Aulnay resisted the attack , and seven of his men were wounded and three killed . La Tour did not attack the fort , which was defended by twenty soldiers . La Tour burned the mill , killed the livestock and seized furs , gunpowder and other supplies . Siege of St . John ( 1645 ) . While La Tour was in Boston , on Easter Sunday 13 April 1645 , d ' Aulnay sailed across the Bay of Fundy and arrived at La Tour ' s fort with a force of two hundred men . La Tour ' s soldiers were led by his wife , Françoise - Marie Jacquelin , who became known as the Lioness of LaTour for her valiant defence of the fort . After a five - day battle , on 18 April , d ' Aulnay offered quarter to all if Francoise - Marie were to surrender the fort . On that basis , knowing she was badly outnumbered , she capitulated and d ' Aulnay had captured La Tour ' s Fort Stainte - Marie . D ' Aulnay then reneged on his pledge of safety for the defenders and treacherously hanged the La Tour garrison while Madame de la Tour was forced to watch with a rope around her neck . Three weeks later , while still in d ' Aulnay ' s hands , she died . With the death of his wife and the loss of his fort , La Tour did not return to Acadia for the next four years , until after d ' Aulnay died in 1650 . Afterward . After defeating La Tour at Saint John , from the capital Port - Royal ( Annapolis Royal ) , d ' Aulnay administered posts at LaHave , Nova Scotia ; Pentagouet ( Castine , Maine ) ; Canso , Nova Scotia ; Cap Sable ( Port La Tour , Nova Scotia ) ; the Saint John River ( Bay of Fundy ) and Miscou Island . He died in 1650 , opening the governorship of Acadia , and prompting La Tour to return . He married d ' Aulnay ' s widow in 1653 , ending the rivalry . The couple had five children , and hundreds of their descendants live in the Canadian Maritimes today . Four years later , Colonel Robert Sedgwick led one hundred New England volunteers and two hundred of Oliver Cromwell ' s soldiers to capture Port Royal , Nova Scotia . Prior to the battle , Sedgewick captured and plundered La Tour ' s fort on the St . John River and took him prisoner .