BackgroundPolygalacturonase (PG), a crucial enzyme involved in pectin degradation, is associated with various plants’ developmental and physiological processes such as seed germination, fruit ripening, fruit softening and plant organ abscission. However, the members ofPGgene family in sweetpotato (Ipomoea batatas) have not been extensively identified.ResultsIn this study, there were 103PGgenes identified in sweetpotato genome, which were phylogenetically clustered into divergent six clades. The gene structure characteristics of each clade were basically conserved. Subsequently, we renamed thesePGsaccording to their locations of the chromosomes. The investigation of collinearity between thePGsin sweetpotato and other four species, containedArabidopsis thaliana,Solanum lycopersicum,Malus domesticaandZiziphus jujuba, revealed important clues about the potential evolution of thePGfamily in sweetpotato. Gene duplication analysis showed thatIbPGswith collinearity relationships were all derived from segmental duplications, and these genes were under purifying selection. In addition, each promoter region of IbPG proteins containedcis-acting elements related to plant growth and development processes, environmental stress responses and hormone responses. Furthermore, the 103IbPGswere differentially expressed in various tissues (leaf, stem, proximal end, distal end, root body, root stalk, initiative storage root and fibrous root) and under different abiotic stresses (salt, drought, cold, SA, MeJa and ABA treatment).IbPG038andIbPG039were down-regulated with salt, SA and MeJa treatment. According to the further investigation, we found thatIbPG006, IbPG034 and IbPG099had different patterns under the drought and salt stress in fibrous root of sweetpotato, which provided insights into functional differences among these genes.ConclusionA total of 103IbPGswere identified and classified into six clades from sweetpotato genome. The results of RNA-Seq and qRT-PCR suggested thatIbPG006,IbPG034andIbPG099might play a significant role in tissue specificity as well as drought and salt stress responses, which showed valuable information for further functional characterization and application of theIbPGs.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12870-023-04272-1.