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All flowering plants have experienced repeated rounds of polyploidy (whole-genome duplication), which has in turn driven the evolution of novel phenotypes and ecological tolerances and been a major driver of speciation. The effects of polyploidy on gene expression have been studied extensively at the level of transcription and, to a much lesser extent, at the level of the steady state proteome, but not at the level of translation. We used polysome profiling by RNA-Seq to quantify translational regulation of gene expression in a recently formed (∼100,000 years ago) allotetraploid (Glycine dolichocarpa) closely related to the cultivated soybean (Glycine max). We show that there is a high level of concordance between the allopolyploid transcriptome and translatome overall but that at least one-quarter of the transcriptome is translationally regulated. We further show that translational regulation preferentially targets …