A system and method which employs atrial discrimination algorithms to distinguish between different atrial arrhythmias occurring in a patient for selecting an optimal pacing therapy corresponding to the type of arrhythmia identified. In response to the detection of an atrial rate above the atrial tracking rate, discrimination criteria are applied to a detected atrial activity signal to distinguish between different types of supraventricular tachycardia, such as fast atrial flutter and other atrial flutter at a relatively slower rate, which may be occurring in the patient. The pacer is controlled to provide pacing therapy to a heart in a manner corresponding to the type of supraventricular tachycardia identified. The output of an atrial discrimination algorithm may be tracked and the trend thereof used to improve therapy timing. Various embodiments are disclosed herein.