The present study investigated the effects of online argumentation scaffolding on students’ argumentation involving hypothetical and theoretical biological concepts. Two types of scaffolding were developed in order to improve student argumentation: continuous scaffolding and withdraw scaffolding. A quasi-experimental design was used with four 8th-grade classes comprising a total of 124 students. Two classes (63 students) were assigned into the continuous scaffolding group, while the other two (61 students) were assigned into the withdraw scaffolding group. All the students participated in online argumentation regarding four units, including two hypothetical concepts and two theoretical concepts. Both online learning process and scientific argumentation assessment results indicated that the continuous scaffolding group performed significantly better in terms of the quality and quantity of argumentation than the withdraw scaffolding group with regard to the hypothetical biology concepts, particularly in generating rebuttal arguments. In addition, the results also showed that both the continuous group and withdraw group students had better argumentation performance with regard to the hypothetical biology concepts than the theoretical biology concepts. Taken together, the study results suggest that learning argumentation through theoretical biology concepts is more difficult than doing so through hypothetical biology concepts.