In this paper we present and justify methodological principles and syntactic criteria to design an annotation scheme for a Persian Treebank. The advantages of the proposed scheme for annotation of the Persian Treebank will be discussed. At the same time, we present the way that different types of linguistic knowledge (morphological, syntactic and semantic) are encoded in the structures of the schema. We will show how this scheme can account for many of the syntactic constructions that appear to be unique to the Persian language.