In this paper, we propose a scheme for anaphora annotation in Hindi Dependency Treebank. The goal is to identify and handle the challenges that arise in the annotation of reference relations in Hindi. We identify some of the issues related to anaphora annotation specific to Hindi such as distribution of markable span, sequential annotation, representation format, annotation of multiple referents etc. The scheme hence incorporates some characteristics specific to these issues in order to achieve a consistent annotation. Most significant among these characteristics is the head-modifier separation in referent selection. The modifier-modified dependency relations inside a markable is utilized for this headmodifier distinction. A part of the Hindi Dependency Treebank, of around 2500 sentences has been annotated with anaphoric relations and an inter-annotator study was carried out which shows a significant agreement over selection of the head referent using the proposed scheme as compared to MUC annotation format. The current annotation is done for a limited set of pronominal categories.