Changes in gene expression contribute to reproductive isolation of species, adaptation, and development and may impact the genetic fate of duplicated genes. African clawed frogs (genus Xenopus) offer a useful model for examining regulatory evolution, particularly after gene duplication, because species in this genus are polyploid. Additionally, these species can produce viable hybrids, and expression divergence between coexpressed species-specific alleles in hybrids can be attributed exclusively to cis-acting mechanisms. Here we have explored expression divergence of a duplicated heterodimer composed of the recombination activating genes 1 and 2 (RAG1 and RAG2). Previous work identified a phylogenetically biased pattern of pseudogenization of RAG1 wherein one duplicate--RAG1beta--was more likely to become a pseudogene than the other one--RAG1alpha. In this study we show that ancestral expression divergence between these duplicates could account for this. Using comparative data we demonstrate that regulatory divergence between species and between duplicated genes varies significantly across tissue types. These results have implications for understanding of variables that influence pseudogenization of duplicated genes generated by polyploidization, and for interpretation of the relative contributions of cis versus trans mechanisms to expression divergence at the cellular level.