The purpose of the study was to investigate how to scaffold students' critical thinking skills in the process of co-writing and co-reflection of wikibooks in formal learning contexts. To observe critical thinking skills in wiki collaborations under different levels of instructional guidance, two graduate wikibook projects were selected: an enhanced scaffolding case (ESC) which involved structured wikibook guidelines and critical feedback exercises, and a minimal scaffolding case (MSC) which involved only basic wikibook guidelines. Quantitative and qualitative data analysis methods were adopted to compare students' perceived and observed levels of critical thinking and participation in wikibook creation. Results showed that participants in the ESC displayed relatively higher critical thinking levels as wikibook authors and peer editors. Participants in the MSC displayed relatively lower critical thinking levels, but showed more active participation in terms of the frequencies of words edited in wikibook chapters. As peer editors, however, students in both cases tended to show low levels of critical thinking and participate passively even though they considered wikibooks to be a useful online collaboration tool. Document and interview analyses revealed that MSC students experienced difficulties developing their wikibooks due to the lack of instructional assistance and displayed more trial and error, which led to their low critical thinking levels and high participation levels. One student with expertise in wikis dominated peer editing in the MSC group, but the ESC group had relatively even contributions among peers in critical thinking and participation because enhanced scaffolding was more effective for those who did not have prior knowledge and experience in wikis or editing.