Because of the increasing number of diverse routing protocols proposed to deal with the network dynamics in mobile ad hoc networks (MANETs), the heterogeneity of MANETs has increased dramatically. While many of these extant proposals only concern enhancing routing in a single domain, little attention has been given to the interoperations among heterogeneous MANETs. Moreover, the existing inter-domain routing protocols (i.e., BGP) that have been designed for the Internet cannot cope with the new challenges derived from the MANETs, such as (1) the rapid dynamic changes of network topology due to mobility, and (2) the larger diversity in intra-domain ad hoc routing protocols. In this chapter, the authors address some of the major challenges and identify new directions to the development of seamless inter-domain routing for enabling end-to-end communications over heterogeneous MANET domains.