Histone ubiquitination plays a central role in regulating eukaryotic transcription. Monoubiquitination of histone H2B is a hallmark of actively transcribed genes whereas monoubiquitinated of H2A is highly enriched in heterochromatin of higher eukaryotes. Histone H2B monoubiquitinated at K123 (in yeast; K120 in humans) is required for histone H3 trimethylation, recruitment of H2A/H2B chaperones, and appropriate transcription activation, elongation and mRNA export. The E2/E3 pair, Rad6/Bre1, monoubiquitinate H2B, whereas several deubiquitinating enzymes specifically remove this modification. In yeast, two deubiquitinating enzymes regulate H2B ubiquitination: the Spt-Ada-Gcn5 acetyltransferase (SAGA) transcriptional coactivator complex, which contains a four-protein subcomplex (Ubp8/Sgf11/Sus1/Sgf73) known as the deubiquitinating (DUB) module that targets H2B; and Ubp10, a single subunit enzyme. Despite the fact that both the DUB module and Ubp10 target the same histone substrate, deletion of the DUB module/Ubp8 and Ubp10 have different phenotypes, suggesting that they play distinct roles. We will discuss biochemical and structural studies of H2B deubiquitinating enzymes that bear on the specificity and potential biological role of these enzymes.