Viroid is a small single stranded circular RNA molecule without protein coat. Because of no coding capacity, it needs to use the RNA polymerase of hosts to replicate itself. It can be disseminated by mechanical transfer, insects, pollen, seeds, etc. International seeds trading are usually long distance, so easily for viroid to be disseminated from countries to countries. Viroids make several economically significant diseases but sometimes it will not induce symptoms, so many countries set quarantine requirements and test imported seeds to avoid viroid spreading. Pospiviroidae, one family of viroid, usually infects Solanaceae crops, e.g. tomato, pepper, potato. In last ten years, there are some disinfectants mentioned in previous study effective for disinfecting seeds to diminish viroid. In this study, three tomato lines and two pepper lines were selected because they were detected viroid-infected after the first disinfection. To do seeds re-treatment, using different concentration of NaOCl and combination of HCl /Trisodium phosphate (TSP) were used to treat seeds with different concentration and time to make totally eight treatments. Infection rate of each line at different treatments were checked by reverse-transcription polymerase chain reaction (RT-PCR) after seeds secondary disinfection. After seeds disinfection, infection rate and germination rate were inspected and analyzed. Infection rate was based on the ratio of infection. Germination rate was determined by when did the cotyledon of seed grow and evaluated whether using those disinfection would destroy seed vigor. According to our data, in tomato lines, using low concentration of NaOCl to disinfect seeds could get lower infection rate instead of using high concentration one, and also have a good germination rate. In pepper lines, using combination of HCl/TSP to disinfect seeds could get better disinfection efficiency, in addition, the germination remain well. In this study, we found the trend that using which treatment is moderate for tomato and pepper, but the best concentration disinfectant and treatment duration combination could be study further in the future.