<p>The presence of viral diseases seriously affects the growth performance of apple rootstocks and reduces the production benefits of the apple industry, highlighting the need for efficient and reliable virus eradication methods. In this study, an integrated virus eradication method based on combining thermotherapy with electrotherapy was established to eradicate apple stem grooving virus (ASGV) and apple chlorotic leaf spot virus (ACLSV) from in vitro apple rootstocks ‘XN-E4’ and ‘XN-E5’. Shoot tips were excised from 4-week-old thermotherapy treated plants, subsequently subjected to electrotherapy, resulting in successful eradication of ASGV and ACLSV. We compared the virus eradication efficiency of thermotherapy combined with either electrotherapy (T+Elec), meristem culture (T + M) or cryotherapy (T+Cryo). The‘T+Elec’ treatment avoids technical proficiency requirements associated with ‘T + M’ and ‘T+Cryo’ and we were able to achieve virus eradication efficiencies, of 33.3% and 50% for ASGV, and 66.7% and 83.3% for ACLSV for ‘XN-E4’ and ‘XN-E5’, respectively. The genetic stability of regenerated plants was evaluated using Inter simple sequence repeat (ISSR) molecular markers, which showed no polymorphic bands between Elec-treated plants and in vitro controls, indicating that the ‘T+Elec’ treatment did not induce detectable genomic variation. Therefore, the ‘T+Elec’ was an efficient and reliable approach for ASGV and ACLSV eradication in two apple rootstocks.</p>