The purpose of this mixed-methods study was to explore how seventh graders in a suburban school in the United States and sixth graders in an urban school in Taiwan developed argumentation skills and science knowledge in a project-based learning environment that incorporated a graph-oriented, computer-assisted application (GOCAA). A total of 42 students comprised the treatment condition and were engaged in a project-based learning environment that incorporated a GOCAA. Of these 42 students, 21 were located in the United States and 21 were located in Taiwan. A total of 26 students comprised the control condition and were engaged in a project-based learning environment without the GOCAA. Of these 26 students, 15 were in the United States and 11 were in Taiwan. In each country, verbal collaborative argumentation was recorded and the students' post-essays were collected. A one-way analysis of variance (ANOVA) was conducted for each measure of science knowledge about alternative energies. The results showed a significant treatment effect for the outcome of scientific explanation among U.S. students, while among Taiwanese students, a significant treatment effect on scientific facts was observed. A one-way ANOVA was additionally conducted for each measure of argumentation skills and a significant treatment effect on counterarguments and rebuttals was observed among the U.S. students, while in Taiwan, a significant treatment effect on reasoning and rebuttals was observed. A qualitative analysis was conducted to examine how the GOCAA supported students' development of argumentation skills in different countries. This study found distinct argumentation patterns between the U.S. and Taiwanese intervention teams. Additionally, a distinct gender difference in the use of evidence and division of labour was noted when the Taiwanese teams were compared with the U.S. teams, which may be explained by cultural differences. This study concluded that, in both the United States and Taiwan, a project-based learning environment incorporating a GOCAA was effective in improving students' science knowledge and developing their scientific argumentation skills.