From their website
Wilderness Permits
John Muir Trail
If you plan to hike the John Muir Trail as a continuous hike, you only need one wilderness permit for the entire trip (you do not need a "Whitney stamp"). Most people begin the hike at Happy Isles (its traditional start in Yosemite Valley), however many people begin at Lyell Canyon (Tuolumne Meadows) because permits for this trailhead are slightly easier to obtain. There is no special JMT permit.
If you plan to hike the John Muir Trail as a continuous hike, you only need one wilderness permit for the entire trip (you do not need a "Whitney stamp"). Most people begin the hike at Happy Isles (its traditional start in Yosemite Valley), however many people begin at Lyell Canyon (Tuolumne Meadows) because permits for this trailhead are slightly easier to obtain. There is no special JMT permit.