In spoken conversation, the frequency of discourse markers (henceforth, DMs) is significant compared to other word forms (Fung and Carter, 2007). Essentially, DMs perform a range of functions in order to ensure that social interaction works smoothly and that mutual understanding is accomplished. In educational settings, DMs perform an important function in providing pedagogical clarification and in promoting effective interaction (Dalle and Inglis, 1990). The present study attempts to reveal that in language classrooms, there is a reflexive relationship between teachers’ use of DMs, classroom interaction, and pedagogical purpose. It examines the ways in which DMs are used and the functions they perform in academic spoken discourse. The data come from nine-hour video recordings of Chinese college EFL classes, recorded as part of a three-year research project “EFL Classroom Discourse Research and Teacher Development” and supported by China National Social Sciences Grants from 2007 to 2009. The spoken corpus is subjected to a multi-layered analytical approach which looks at both macro (text) and micro (word) levels, and which uses the principles of conversation analysis (CL) and corpus linguistics (CA), together with second language (L2) classroom modes analysis. The appropriateness of adopting a combined CL and CA approach is based on a number of factors including the linguistic properties of DMs as lexical bundles (Biber and Conrad, 2002), a recognition of their multi-word nature (McCarthy, 2006), and their high frequency of occurrence in conversational practices (Schiffrin, 2003). Using a multi-layered analysis has resulted in a number of findings which might not have emerged by using a single mode of analysis. The study presents the linguistic and contextual patterns of DMs across various classroom micro-contexts, and highlights differentiated interactional features in relation to classroom pedagogy. This study has important implications for future research regarding curriculum design, EFL teacher training and education, specifically in its potential to help teachers achieve their pedagogical goals.