Endosomal sorting of ubiquitinated membrane proteins for trafficking to lysosomes is executed by a complex of two ubiquitin-binding proteins, Hrs and STAM, that localizes on a microdomain of early endosomes with a flat clathrin coat. AMSH is a deubiquitinating enzyme that interacts with STAM and is implicated in the down-regulation of epidermal growth factor receptor. AMSH has a close homolog, AMSH-like protein (AMSH-LP). Here we show that AMSH-LP is also a deubiquitinating enzyme that acts on early endosomes. We further show that AMSH and AMSH-LP bind to the terminal domain of clathrin heavy chain via a novel clathrin-binding site conserved between these proteins. Exogenously expressed AMSH and AMSH-LP co-localized with clathrin on early endosomes. However, deletion of the clathrin-binding site from the proteins, as well as RNA interference-mediated depletion of clathrin heavy chain, resulted in a failure of AMSH and AMSH-LP to localize on endosomes. In contrast, a mutant of AMSH that lacks the ability to bind STAM localized normally on endosomes. We suggest that AMSH and AMSH-LP are anchored on the early endosomal membrane via interaction with the clathrin coat.