The purpose of this study is to monitor genetically modified bean sprouts at traditional markets in Seoul and to investigate perception of traditional market merchants and high school students on genetically modified organisms (GMOs). We analyzed 30 bean sprouts that were selected at 11 traditional markets in Seoul using the method of polymerase chain reaction (PCR). Also, we compared perception of GMOs between merchants (n = 30) and students (n = 126). Knowledge test about GMOs was performed by students. The result of PCR, 16.7% of bean sprouts were confirmed as GM bean sprouts (n = 5). Students had significantly more exposure to information about GMOs than merchants (p < 0.05). Major information sources about GMOs were from mass media (television, newspaper and radio). About half of subjects were not aware that they eat GMOs and GMOs are sold to consumers. Only 17.3% of subjects had constant eating intent for GMOs after perceiving foods that he/she usually eats are GMOs. 51.3% of subjects had willingness to purchase GMOs if GMOs have same quality and lower cost than natural foods. 37.2% of subjects thought that GMOs would be harmful to humans. Students had more positive perception of GMOs' side effects than merchants (p < 0.01). There was no merchant who knew labeling of GMOs. 19.1% of students knew labeling of GMOs. Students' mean percentage of correct answers of six questions about GMOs was 45.2%. Therefore, providing adequate information about GMOs is needed for consumer's choice whether to purchase GMOs or not.