A robust method of identifying and linking footnote and its reference in the text is proposed to solve the footnote recognition problem. Novel features of the footnote, including page layout, font information, lexical and linguistic features, are utilized for the task. Clustering is adopted to handle the features which vary in different kinds of documents but stable within one document so that the process of identification is adaptive with document types. In addition, this method leverages results from the matching process to provide feedback to the identification process and further improves the algorithm accuracy. The primary experiments in real document sets show that the proposed method is promising to identify footnote in a PDF document.