Many educators, throughout history, believe that skillful thinking is one of the important goals in education. Contemporary societies often require people to possess not only remarkable knowledge but also strong thinking skills, often referred to as critical thinking or higher order thinking skills. This study used a mixed-method approach to investigate the effects of integrating LCs (LC) into freshman English classes on cultivating critical thinking skills among 57 Taiwanese university students studying English as foreign language (EFL). This study also intended to examine the difference between in-class and the Messenger (superscript TM)-mediated LC discussions in developing critical thinking skills, and to explore the students' perceptions of LC discussions after their one-year participation.This paper presentation draws on research data from a year-long study of two freshman English for non-major (FENM) classes. These data comprise a questionnaire survey, LC discussion transcripts, and the archives of instant messenger. Two groups of students, Messenger (superscript TM) (MSN)-mediated and in-class, face-to-face LC discussions were compared in terms of the degree of their higher-order thinking as reflected in the questions raised by the participants during their LC discussions. Participants' critical thinking was measured by referring to the Hierarchy of Bloom's Taxonomy. Pretest and posttest of the participants' self-assessment on Critical Thinking were calculated. Proportions of six levels of hierarchical thinking reflected in the discussion questions from 4 participants were presented in bar charts to show the progression as the semester unfolded.The results from this study suggest that infusing LCs into freshman English classes helps EFL students enhance their critical thinking. This study offered EFL teachers better understanding of how face-to-face and online LCs benefited students through discussing and sharing their own thoughts in English within a small group. The connection between critical thinking and LC offered valuable insights for educators, researchers, and schools concerned with implementing LCs in English teaching, especially those who have a desire to help EFL students improve both their reading and thinking skills.