This study aimed to examine middle school students’ epistemological beliefs, argumentation quality in genetically modified organisms (GMO), and their relationship. A correlational research approach was used. The Epistemological Beliefs Questionnaire (EBQ) was used to obtain students' scores concerning epistemological beliefs. Students’ argumentation qualities in GMO were collected through the genetically modified organisms task developed by Xiao, 2015. Analysis of the data revealed that although students showed mid-quality arguments, the argumentation quality score was mainly obtained from their justification scores. Students had fairly sophisticated epistemological beliefs in all dimensions of the questionnaire. The argumentation quality of students showed significant relationships between each dimension of epistemological beliefs (source/certainty, development, justification). Multiple regression analysis revealed that one of the dimensions of epistemological beliefs (justification) significantly predicted students’ argumentation quality in genetically modified organisms. It can be concluded that socioscientific issues can be used more frequently to improve students’ epistemological beliefs and argumentation qualities. In this way, students can learn to make informed decisions with the help of socioscientific argumentation.