Background Wnt signaling is a key regulator of development and tumorigenesis. Protein phosphatase 2A (PP2A), which consists of a catalytic C, a structural A, and a regulatory B subunit, plays diverse roles in Wnt signaling through its B56 subunits. B56 is a multigene family encoding for proteins with a conserved core domain and divergent amino- and carboxy-termini. Ectopic B56α and B56γ reduce β-catenin abundance and B56α reduces Wnt-dependent transcription, suggesting that B56α and B56γ inhibit Wnt signaling. In contrast, B56ε is required for Wnt signaling. Knowledge of where and when B56 subunits are expressed during Xenopus development will aid in our understanding of their roles in Wnt signaling. Results We have undertaken expression analyses of B56α and B56γ in Xenopus laevis. We cloned Xenopus B56α; it is 88% identical to human B56α. Xenopus B56γ is 94% identical with human B56γ, however, a novel evolutionarily conserved mixed-isoform transcript was identified that contains a B56δ-like amino-terminal domain and a B56γ core domain. The B56δ-like variable domain exon is located upstream of the B56γ variable domain exon at the human B56γ locus, suggesting that the mixed-isoform transcript is due to alternative splicing. B56γ transcripts with different 3' ends were identified that lack or possess a 35 base pair sequence, resulting in either a transcript similar to human B56γ1, or an uncharacterized evolutionarily conserved sequence. Real time RT-PCR analyses revealed that B56α is expressed at moderate levels before the midblastula transition (MBT), at reduced levels during gastrulation and neurulation, and at high levels during organogenesis, while B56γ is expressed at low levels until organogenesis. B56α is enriched in the ventral hemisphere pre-MBT, while B56γ is ventrally enriched post-MBT. Aα, Aβ, Cα and Cβ are expressed in early Xenopus development, suggesting the presence of a functional heterotrimer. Conclusion Our data suggest that B56 functional diversity is achieved in part through the synthesis of a novel mixed-isoform B56δ/γ transcript. Our data also suggest that B56α functions pre-MBT, inhibiting Wnt signaling on the ventral side of the embryo, and again during organogenesis, while B56γ functions primarily post-MBT.