Ubiquitin-specific proteases (UBPs) are a highly conserved family of proteins in eukaryotes, and play critical roles in protein de-ubiquitination. Here we report a systematic genetic and expression profiling analysis of the UBP gene family in the Arabidopsis thaliana genome. Mutation analysis of 25 of the 27 member genes representing 13 of the 14 sub-families of the UBP gene family revealed that single-gene mutants of three genes in two sub-families exhibit visible phenotypes. Two of these three genes belonging to the UBP15 sub-family were selected for further characterization. The ubp15 mutants display narrower, serrated and flat rosette leaves, partially due to a defect in cell proliferation, as well as other phenotypes such as early flowering, weak apical dominance and reduced fertility, while the line over-expressing UBP15 shows opposite phenotypes. We demonstrated that UPB15 has UBP activity in vitro, and that this biochemical activity is essential for its in vivo function. A genetic interaction analysis among members of this sub-family revealed that UBP15 and UBP16, but not UBP17, have functional redundancy. Our data thus suggest that distinct UBPs, even within a closely related sub-family, can function in different developmental pathways. Although there are clearly functional redundancies among related sub-family members, those redundancies cannot be inferred simply based on the amino acid identity of the family members.