Though we have advocated explicit argumentation instruction in science classes for decades, daily instructions are still found insufficient in improving students' argumentation competence. It is therefore important to explore effective instructional strategies through classroom research. This paper compares instructional strategies for classroom argumentation. We report on a quasi-experiment conducted with tenth-grade students (n = 92) that compares "adversarial" and "parallel" argumentation designs for the topic "genetic inheritance," an inquiry-based socio-scientific issue (SSI) unit. The instruction was conducted through the online platform, Web-based Inquiry Science Environment (WISE). In the "parallel" design, student dyads were assigned to the same initial stances and were asked to change to multiple perspectives together, while in the "adversarial" design, students were assigned to opposite stances, and a debate was launched between the two sides. Students' overall argumentation performance improved significantly in both cases, yet the progress was greater in terms of "counterarguments" for students in the "parallel" design. Such findings highlight the value of "parallel" thinking in developing students' argumentation competence, especially in producing "counterarguments." Suggestions on instructional design for scientific argumentation activities are proposed accordingly.