Sweet potato is one of the most important food crops with strong environmental adaptability. Protein phosphatase 2A (PP2A) is a major intracellular protein phosphatase that plays crucial roles in hormone signal transduction and abiotic stress response. Characterization of PP2A can elucidate the mechanisms of stress resistance in this crop. In this study, a total of 15 PP2A transcripts, including nine regulatory subunit-encoding sequences and six catalytic subunit-encoding sequences, were identified from sweet potato and found to be expressed at varying levels. Only one contained a complete open reading frame and encoded a B regulatory subunit (termed IbPP2A1). Ten polymorphic sites were distributed in the coding region of this gene, but most did not result in amino acid change. RNA sequencing-based digital gene expression profiling showed that this PP2A gene was primarily expressed in fibrous roots and developing tuberous roots under natural conditions. After drought, salinity, and alkaline stress treatment, the expression of IbPP2A1 was obviously upregulated in stems and tuberous roots at 2 days, whereas the expression of IbPP2A1 in leaves was only upregulated by drought stress at 2 days. However, heterogeneous expression of IbPP2A1 did not enhance abiotic stress tolerance in recombinant Saccharomyces cerevisiae. The results described here indicate that IbPP2A1 is an abiotic stress-responsive gene, but it could not work alone in vitro. This study provides a preliminary but global insight into PP2A proteins in sweet potato for further investigations on improving stress tolerance in this crop.