Vacuolar processing enzymes (VPEs) are important cysteine proteases and function in the processing and maturation of protein precursors, plant senescence and immunity, programmed cell death, as well as sugar accumulation. This paper investigated VPEs in pear and identified as a key finding eight members of the VPE family in the pear (Pyrus) genome, and their gene structure, protein conserved domains and phylogenetic relationship were analysed by bioinformatics methods. Further key findings were that two of these VPEs (PbrVPE2 and PbrVPE5) represented a vegetative and the others a seed-coat type VPE. Transcriptome data and quantitative real-time PCR were used separately to analyse the expression patterns of the pear VPE gene family. The PbrVPE2 and PbrVPE5 were, in comparison to the other VPEs, abundantly expressed by possibly playing a role during the development and ripening of the pear fruit. A highly expressed PbrVPE2 gene was isolated from a pear fruit and named PpyVPE2. The biological function of the newly PpyVPE2 genes was predicted by recombinant protein expression and subcellular localisation.