Between the beginning and end of the 11th/17th century, that part of the Maghrib known today as Morocco went through a series of profound political shifts, beginning with the death of the Sa’adian ruler Ahmad al-Mansur in 1603. Al-Mansur, who had expanded Sa’adian rule through West Africa as far south as Timbuktu, and who had maintained continuous diplomatic relations with both European powers and the Ottoman Empire, was the last ruler of his dynasty to enjoy uncontested rule over the Farthest Maghrib. Following his death, political control was disputed by his sons, and the first two thirds of the 17th century saw Morocco divided into a number of political spheres, including the corsair state of Rabat/Sale, populated in part by a large number of Moriscos who had settled there following their final expulsion from Spain in 1611. Morocco was only political re-united, and then as a much smaller geographical area, in 1668 with the rise of the Alawite dynasty, which continues to rule Morocco today. This paper will explore the broad outlines of intellectual activity in Morocco during this period of transition, beginning with the dissolution of the Sa’adian dynasty and ending with the beginning of the 19th century and the increase of European influence over the Alawites. Whereas Moroccan intellectual history during this period has often been glossed as a series of developments within Sufism, it will discuss the relationship between Sufism and the rational sciences, including logic, and philosophy in general, as well as in theology and law. Building on a discussion of the career and influence of the influential Sufi, logician, and theologian al-Hasan al-Yusi (d. 1691) — himself chiefly known in contemporary scholarship for his letter publicly reprimanding the second Alawite ruler, Moulay Ismail —I aim to offer an overview of the ways in which intellectual and political trends interacted in Morocco that will provide a productive comparison with events taken place within the various provinces of the Ottoman Empire.