Ubiquitination is a post-translational modification of proteins that plays an essential role in many cellular processes. Ubiquitination involves the attachment of the small polypeptide ubiquitin to target proteins to control their activity or stability. As a reversible modification, E3 ubiquitin-ligases attach ubiquitin to proteins while deubiquitinases (DUBs) remove ubiquitin from tagged proteins. Revealing the mechanisms that regulate ubiquitination/deubiquitination is important for understanding how cells fine-tune protein activity to control important processes and pathways. It is clear in animals and yeast that WD-repeat proteins (WDR) bind to and activate DUBs. In plants, however, no interactions between WDR proteins and DUBs have been reported. Here, we used BLAST searches to identify plant homolog proteins of a conserved animal DUB and its associated WDR proteins. Based on these homologies, we predicted that Arabidopsis UBP3, a DUB involved in pollen development and transmission, forms a complex with the WDR proteins At2g37160 and LRS1. Indeed, these three proteins could be co-immunoprecipitated when transiently co-expressed as epitope-tagged proteins in plant cells. At2g37160 also interacted with UBP3 in the yeast two-hybrid system and could enhance the DUB activity of UBP3 ten-fold in vitro. These results provide the first evidence that plant DUBs, like animal DUBs, are regulated by WDR proteins.