This paper explores several important issues in developing syntactically annotated Korean corpora for higher-level language processing, including semantic-discourse parsing, question-answering, machine translation, information retrieval, etc.In particular, we compare the Penn Korean Treebank (PKT) and the Korean Treebank of the 21st Century Sejong Project (ST) and discuss four critical issues in syntactic annotation.We argue for the use of more sophisticated morphosyntactic information, and based on our comparative study, we propose revisions in the syntactic annotation schemes of the existing Korean Treebanks in order to improve the quality of annotated corpora and their usability both for conducting theoretical research and for developing computational tools.The results of our comparative study reveal four significant issues in syntactic annotations: the syntactic analysis of verbal complexes, the hierarchical structure of noun phrases, the representation of traces, and the marking of zero elements.These factors may trigger erroneous syntactic representations for certain linguistic phenomena, and they may increase difficulties in data search and lessen reliability in computational processing.Thus, evaluating and improving the syntactic annotation of Treebanks is an important task for aspects of both theoretical and computational linguistics.