Ubiquitination is a prevalent posttranslational modification in eukaryotic cells. Ubiquitination almost regulates all eukaryotic signaling pathways, thereby playing essential roles in eukaryotic cellular processes including immune responses. Bacterial pathogens inject a series of virulence proteins, named effectors, via special protein secretion systems, such as typeⅢ and typeⅣ secretion systems, into the host cells to modulate host signaling pathways. Many effectors harbor unique enzymatic activities to modify ubiquitin or the ubiquitin-conjugating enzyme Ubc13, or have E3 ubiquitin ligase or deubiquitinase activities. This review summarizes the progresses and the newest discoveries on mechanisms of host ubiquitination modulation by bacterial effector proteins.