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Protein ubiquitination is common and crucial in cellular functions, however, little is known about how deubiquitinating enzymes (DUBs) reverse regulate the ubiquitination signaling process. <i>PPPDE</i> family proteins are a novel class of deubiquitinating peptidases with demonstrated deubiquitination/deSUMOylating activities. In this study, we identified 10 <i>PPPDE</i> genes from the rice (<i>Oryza sativa</i> L.) genome unevenly distributed on five chromosomes, where most of these members have not been reported to date. Based on the gene structure, the <i>OsPPPDE</i> family consists of three distinct subgroups within the phylogenetic tree. <i>Cis</i>-element analysis identified light/phytohormone-responsive, development, and abiotic stress-related elements in the promoters of <i>OsPPPDE</i>. Furthermore, we conducted and analyzed the transcript abundance of <i>OsPPPDE</i> under various tissues and stresses using the transcriptome data of 352 samples from the Rice Expression Database and GEO datasets. Moreover, <i>OsPPPDE5</i> showed differential regulation of its transcript abundance during Cd and drought stress. Collinearity and syntenic analysis of 101 <i>PPPDE</i>s and <i>PPPDE</i>-like proteins in 10 plant genomes indicated that this family is evolutionarily conserved. Domestication analysis suggests that <i>OsPPPDE</i>s may contribute to <i>indica–japonica</i> divergence using the data from the 3K Rice Genome Project. Our study provides a foundation for further study on the function and molecular mechanism of the <i>OsPPPDE</i> gene family.