Hypertrophic cardiomyopathy (HCM) is a genetic disease of the cardiac sarcomere with an autosomal dominant pattern of inheritance. Patients with HCM are at high risk of developing atrial fibrillation (AF) particularly in the setting of advanced diastolic dysfunction and left atrial enlargement. AF is a marker of increased mortality and morbidity and results in a significant reduction in quality of life. Antiarrhythmic medications improve symptoms and reduce AF recurrence, but few are safe and there exists little data to guide their long-term use in HCM. Non-pharmacologic approaches have emerged and have equal or greater efficacy than pharmacologic approaches. Although these approaches are promising, the long-term impact on atrial function needs to be carefully studied as it may impact quality of life in patients that age in the setting of a progressive diastolic disease disorder. Nonetheless, with the significant impact of AF in HCM, rhythm control strategies are often required. The understanding of rhythm control strategies in HCM, an often rapidly progressive diastolic dysfunction disorder, may provide insight in how to treat the much more prevalent AF patient with hypertensive cardiomyopathy. Regardless of treatment strategy (rhythm or rate control) patients are a moderate to high risk of thromboembolism and until data are available to suggest otherwise require long-term warfarin anticoagulation.