Political instability and a theological crisis in France led to the outbreak of civil war in 1562 in the first of eight consecutive wars known as the Wars of Religion. The royal edicts of pacification that ended these wars were variously praised or condemned for granting liberté de conscience to French subjects. This dissertation establishes that the monarchy instituted a limited idea of liberty of conscience starting in 1563 in order to avoid granting French Protestants the full legal privileges of a corps - a rights-bearing association characteristic of old regime societies – and officially recognizing their church. This toleration was legally implemented through the Gallican kings’ earlier secularization of heresy prosecution combined with the royal ability to grant privileges to French subjects. In the end, the monarchy’s limited toleration separated the freedom of an individual’s conscience from the right of a church to assemble for worship. This royal policy of not forcing consciences was in opposition to both full toleration of a second religion in France and continuing to persecute Calvinists as heretics. It also separated citizenship from Catholicity. This new Calvinist citizenship was perceived as a direct threat to both the Catholic Church and the French polity. In this dissertation, the problem of toleration is seen through the battle over where the boundaries of conscience ended and began, which correlated with a debate about French citizenship, but also about what was and was not proper religion. It demonstrates that these two things were interrelated: to be a French citizen meant having access to a range of Gallican institutions, from various types of assemblies to the French Church itself. Calvinists wanted their own church as well as continued access to the politico-theological public sphere created by these Gallican institutions. The idea that conscience could be free while worship was limited was not recognized by the majority of Protestants to whom it was granted. Toleration and the risk of pluralism was seen by many French subjects, Catholic and Protestant, as a direct threat to the polity. Liberty of conscience was used to try and get around the problem of pluralism by bounding conscience in the household; this dissertation explores how this dialectic between sovereignty and private property instantiated in the household was both the logic of liberty of conscience and that of logic for the basis of citizenship through the household in Jean Bodin’s 1576 Les six livres de la République. By juxtaposing this theoretical argument with Bodin’s role in the debates over liberty of conscience and property in the 1576 Estates General, the centrality of liberty of conscience in both defining French citizenship in a plural France and its deep connection to the practice of absolute royal power is revealed. By rejecting the mapping of a rational/irrational dichotomy onto a political/ religious one, the Catholic League’s rejection of a Protestant king through the adoption of Huguenot resistance theory and communal action in individual towns can be seen as the rejection of the private/public boundary of conscience that de-Catholicized French citizenship and the re-drawing of that boundary around their communal corps and, ultimately, the kingdom. Henri IV’s eventual victory over the Catholic League and conversion to Catholicism can be seen as a triumph for Gallican institutions and a confirmation that the politico-theological sphere would remain Catholic. French Calvinists continued to fight for inclusion as full members of the polity through the Reformed General Assemblies that negotiated with Henri IV after his conversion in 1593. Because their ability to participate relied upon the king’s sufferance, Protestant institutional resistance to limited liberty of conscience had the obverse effect of its intention; Calvinist institutional self-organization both mirrored and strengthened the role of centralized monarchical institutions. Its conclusion determines that the battle over the boundaries of conscience resulted in strengthening the monarchy from the bottom up, while freedom of conscience itself, long seen as the hallmark of nascent individual rights in the 1598 Edict of Nantes, was really a rejection of religious pluralism imposed on French subjects from the top-down. This early example of individual religious rights in the sixteenth century demonstrates to what degree civil rights are constructed and negotiated, and in what ways they can be circumscribed by their very existence.