A method, apparatus, and computer instructions for managing multi-threaded conversations in an instant messaging system. The present invention provides a menu option to allow the start of a new topic of discussion within the current instant messaging session. When a new topic is selected, a new thread of conversation is created within the messaging window that is segregated from previous topics of discussion. This new thread of conversation may be created at all other locations for all of the parties involved in the instant messaging session. In this manner, each party to a messaging session containing multiple conversations may be able to understand which response is related to which thread of conversation. In addition, a menu option may be provided by the instant messaging application to allow a user to merge one or more of the threaded conversations into a single conversation.