This study examined how students' scientific argumentation changed over as they participated in hierarchy of inquiry learning. The hierarchy of inquiry is a comprehensive approach in which students working for anextended period of time that integrated several ways of inquiry systematically to investigate and respond to a complex question, problem, or challenge. This action research was conducted in Biology Teacher Education Program Faculty of Teacher Training and Education Sebelas Maret University. The students, who were at the 4rd semester and who studied the class of Plant Embryology, were purposely selected. The data were collected from interviews with the researchers, classroom observations, and collection of student portfolios. The scientific argumentation was measured using modified Toulmin's Argument Pattern (TAP) with four kinds of argument elements: claim, evidence, reasoning, and rebuttal which presented in oral and written. The results showed that students who experienced with the hierarchy of inquiry performed better scientific argumentation which reflecting their higher-order thinking abilities. We conclude that hierarchy of inquiry is possible in fostering student's scientific argumentation, doing some inquiry activities, and thus make a positive impact on scientific argumentation ability . The findings can be helpful in the process of designing the new curricula for teacher candidates in order to foster scientific inquiry.