In this paper we introduce the concept of Adaptive Orthogonal Frequency Division Multiplexing (AOFDM) for two-way relay systems. In order to implement AOFDM at the nodes, the Channel State Information (CSI) is required. Usually CSI is estimated and hence the effect of estimation error should be considered while implementing AOFDM. In the case of two-way relay, channel estimation at the nodes usually result in the overall channel between the source and relay. But for implementing AOFDM, we require the individual channel between node and relay. We propose a simple method to obtain the individual channel assuming that the estimate of combined channel is available. The loading algorithm used is the Levin-Campello loading algorithm. But the general frame work provided by us can be used to implement other loading algorithms for two-way relay systems. © 2013 IEEE.