Part of Speech (POS) annotation is a significant challenge in natural language processing. The paper discusses issues and challenges faced in the process of POS annotation of the Marathi data from four domains viz., tourism, health, entertainment and agriculture. During POS annotation, a lot of issues were encountered. Some of the major ones are discussed in detail in this paper. Also, the two approaches viz., the lexical (L approach) and the functional (F approach) of POS tagging have been discussed and presented with examples. Further, some ambiguous cases in POS annotation are presented in the paper.