Intellectual property rights should not be regarded as an instrument alien to traditional peoples for the protection of their knowledge systems generally and in this paper traditional medicine knowledge specifically when they deem it appropriate. It is important to ensure traditional medicine practitioners and their knowledge systems are not neglected at the national, regional and international levels. A bottom up approach which investigates the use of traditional medicine knowledge and protection mechanisms at the communal, national and regional levels prior to and after western influence (colonisation) is proposed. A top down approach cannot be avoided due to interactions with countries of the North in matters relating to knowledge and resources found in Africa. This paper examines the protection of traditional medicine knowledge systems in Nigeria and Africa; proposing that Africa should aspire to recover control over the use of its traditional medicine knowledge systems in healthcare delivery and drug development through available protection mechanisms.