Allopolyploid genomes are divided into compartments called subgenomes that are derived from lower ploidy ancestors. In African clawed frogs of the subgenus Xenopus (genus Xenopus), allotetraploid species have two subgenomes (L and S) with morphologically distinct homoeologous chromosomes. In allotetraploid species of the sister subgenus Silurana, independently evolved subgenomes also exist, but their cytogenetics have not been investigated in detail. We used an allotetraploid species in Silurana—Xenopus calcaratus—to explore evolutionary dynamics of chromosome morphology and rearrangements. We find that the subgenomes of X. calcaratus have distinctive characteristics, with a more conserved a-subgenome resembling the closely related genome of the diploid species X. tropicalis, and a more rapidly evolving b-subgenome having more pronounced changes in chromosome structure, including diverged heterochromatic blocks, repetitive sequences, and deletion of a nucleolar secondary constriction. Basedon these cytogenetic differences, we propose a chromosome nomenclature for X. calcaratus that may apply to other allotetraploids in subgenus Silurana, depending on as yet unresolved details of theire volutionary origins. These findings highlight the potential for large-scale asymmetry in subgenome evolution following allopolyploidization.