Syntenin-1 is a PDZ domain-containing adaptor that controls trafficking of transmembrane proteins including those associated with tetraspanin enriched microdomains. We describe the interaction of syntenin-1 with ubiquitin through a novel binding site spanning the C-terminus of ubiquitin, centered on Arg72, Leu73 and Arg74 A conserved LYPSL sequence in the N-terminus, as well as the C-terminal region of syntenin-1 are essential for binding to ubiquitin. We present evidence for the regulation of this interaction through syntenin-1 dimerization. We have also established that syntenin-1 is phosphorylated down-stream of Ulk1, a serine-threonine kinase that plays a critical role in autophagy and regulates endocytic trafficking. Importantly, Ulk1-dependent phosphorylation of Ser6 in the LYPSL prevents the interaction of syntenin-1 with ubiquitin. These results define an unprecedented ubiquitin-dependent pathway involving syntenin-1 that is regulated by Ulk1.