This paper proposes a basic scheme for annotating anaphoric relations in Japanese conversations. More specifically, we propose methods of (i) dividing discourse segments into meaningful units, (ii) identifying zero pronouns and other overt anaphors, (iii) classifying zero pronouns, and (iv) identifying anaphoric relations. We discuss various kinds of problems involved in the annotation mainly caused by on-line processing of discourse and/or interactions between the participants. These problems do not arise in annotating written languages. This paper also proposes a method to compute topic continuity based on anaphoric relations. The topic continuity involves the information status of the noun in question (given, accessible, and new) and persistence (whether the noun is mentioned multiple times or not). We show that the topic continuity correlates with short-utterance units, which are determined prosodically through the previous annotations; nouns of high topic continuity tend to be prosodically separated from the predicates. This result indicates the validity of our annotations of anaphoric relations and topic continuity and the usefulness for further studies on discourse and interaction.