This paper describes the process of annotation of 996 lexical bundles (LB) assigned to 39 different discourse functions in a Spanish academic corpus. The purpose of the annotation is to obtain a new Spanish gold-standard corpus of 1,800,000 words useful for training and evaluating computational models that are capable of identifying automatically LBs for each context in new corpora, as well as for linguistic analysis about the role of LBs in academic discourse. The annotation process revealed that correspondence between LBs and discourse functions is not biunivocal and that the degree of ambiguity is high, so linguists’ contribution has been essential for improving the automatic assignation of tags.