Jupiter has persistent northern and southern X-ray auroral hot spots observed by XMM-Newton and Chandra observatories. The observations from 2016 and 2007 show that the northern and southern hot spots exhibit different and independent characteristics, such as different periodic pulsations and uncorrelated brightness changes. Mapping of the X-ray emissions indicates they originate from different local time sectors in Jupiter's magnetosphere, beyond 60 Jupiter radii, challenging current models that the hot spots are generated by the same magnetospheric processes.