As part of a research project that aims to identify the similarities and differences between Web-based and print journal-based scholarly communication, this paper compares the intellectual structure of the XML research field revealed from author co-citation analysis of research papers published on the Web as indexed by ResearchIndex and that derived from print journals as indexed by SCI. Considerable differences are observed and some media specific features are identified. Results from this study demonstrate the importance and the feasibility of the use of multiple data sources in citation analysis studies of scholarly communication, and evidence a “two tier” future scholarly communication system.