Deconjugation of ubiquitin and/or ubiqutin-like modified substrates is essential to maintain a sufficient free ubiquitin within the cell. Deubiquitinases (DUBS) play a key role in the process. Besides, DUBs also play several important regulatory roles in cellular processes. However, our knowledge of their developmental roles are limited. The report here aims to study their potential roles in craniofacial development. Based on the previous genome-wide study in 2009, we selected 36 DUBs to perform the morpholino (MO) knockdown in this study, followed by the Alcian blue cartilage staining at 5 days post-fertilization (dpf) larvae to investigate the facial development. Results classified the tested DUBs into three groups, in which 28% showed unchanged phenotype (Class 1); 22% showed mild changes on the branchial arches (Class 2A); 31% had malformation on branchial arches and ethmoid plate (Class 2B); and 19% had severe changes in most of the facial structures (Class 3). Lastly, we used uchl3 morphant as an example to show that our screening data could be useful for further functional studies. To summarize, we identified new craniofacial developmental role of 26 DUBs in the zebrafish. (C) 2017 Elsevier Inc. All rights reserved.