Citrus production in Florida continues to decline steadily, since the arrival of Huanglongbing (HLB or citrus greening). HLB does not kill the tree, but HLB-infected trees become less productive. Since now, there is no cure for this disease. However, several strategies have been developed to manage and control HLB-infected citrus trees. We have developed and evaluated a heat thermotherapy system (short-term solution) for sustaining productivity of HLB-affected trees. This system heats the canopy and the roots of the trees for a predetermined time and temperature to kill the bacteria. In order to develop an efficient thermotherapy system for treating the tree roots, we first need to know the location and the structure of the roots. In this study, we utilize a ground penetrating radar (GPR), a noninvasive imaging, to construct the map of the root system of a citrus tree in the field. Additionally, we used this system to evaluate several citrus rootstocks and their ability to be HLB-tolerant. The GPR system can develop a high-resolution map of the internal structure of the tree trunk and the rooting system/mass. We have evaluated two antennas with frequencies: (i) 900 MHz (up to 1 m penetration); (ii) 1.6 GHz (up to 0.5 m penetration; better resolution than the 900 MHz). Several maps of citrus tree rootstocks were created to visualize and evaluate the root morphology of HLB-infected trees.