Summary We evaluated the effects of treatments with thermotherapy (80°C for 24 h) and dipping in sodium hypochlorite (NaOCl; 0.8% for 10 min) on the germination percentage, germination rate, vigour index and ToMV inactivation of seeds from three pepino (Solarium muricatum) accessions (96–5, B–2 and OV–8) and two wild relatives (S. tabanoense EC–26 and S. caripense EC–40). Thermotherapy decreased the germination percentage (especially in the wild species), germination rate in wild species but not in cultivated pepino, and vigour index in all cases. Sodium hypochlorite increased germination, except for nonthermotreated seeds of OV–8, improved the germination rate in wild species and the vigour index in all cases except for non thermotreated OV–8. Seed coats were altered by both treatments, especially by NaOCl. Thermotherapy was totally effective in the inactivation of seed‐borne ToMV, while NaOCl was not. Thermotherapy combined with NaOCl allows effective seed disinfection of S. muricatum seeds without negatively affecting seed germination. For the wild species, although thermotherapy reduces germination, the higher number of seeds per fruit in these species reduces the magnitude of the problem. Even when no disinfection is necessary, treatments with NaOCl are always advisable as they improve germination.