During the 1670s, the navy was the focus of increasingly critical scrutiny from parliament and the political nation. This article considers the causes and nature of this criticism, which had its roots in the perceived dominance of the catholic James, duke of York, in the field of naval appointments, and examines the political context of the various inquiries into the state of religious affection in the fleet. By so doing, the article identifies a dilemma which confronted the crown's opponents in the period 1678–81, namely the conflict between the requirement for a strong navy to oppose France and the risk that, because of York's influence over it, that same navy might in fact be an instrument of French and catholic designs. Finally, the response of the officers and men of the navy to the events of the popish plot, exclusion crisis and ‘tory reaction’ is examined, placing the navy in the mainstream, rather than on the periphery, of the political and religious history of the period.