Sna3p and Sna4p are small proteins of unknown function possessing two transmembrane domains and belong to a small family of conserved proteins present in plant and fungi. The budding yeast has four SNA proteins (Sna1–4) that have different localizations in the cell. Sna3p is targeted to the vacuolar lumen by the multivesicular body pathway. Two observations marked Sna3p as a multivesicular body cargo that is sorted in an ubiquitin-independent manner. First, Sna3p-GFP is still correctly transported to internal multivesicular body vesicles under conditions of ubiquitin depletion, which impairs multivesicular body sorting of certain other cargoes. Second, a mutant form of Sna3p-GFP lacking the only potential positions for ubiquitylation is still correctly targeted to the vacuolar lumen. It has thus been postulated that ubiquitylation marks, but not all, membrane proteins for sorting into the interior of the vacuole. In this study we present a further characterization of the Golgi to vacuole trafficking of Sna3p together with its ubiquitylation status. We observed that Sna3p physically interacts with the E3 ligase Rsp5p and that this interaction is essential for sorting of Sna3p to the endosomal pathway. Sna3p is ubiquitylated on its Lys125 residue by Rsp5p and modified by Lys 63-linked ubiquitin chains. In contrast to the conclusions from prior reports, we demonstrated that, as noticed for most other multivesicular body cargoes, Sna3p ubiquitylation is required for its multivesicular body sorting. Sna4p is localized to the vacuolar membrane and interior. Sna4p contains an acidic di-leucine motif, that could be a sorting signal specific for AP-3 dependent pathway directing Sna4p to the vacuolar membrane. In apm3∆ cells, where µ subunit of the AP-3 complex is deleted, Sna4p is missorted to the vacuolar interior. Strikingly, this localization is different from localization of markers of AP-3 dependent pathway. This dissimilarity indicates that Sna4p possesses an additional characteristic, absent in other AP-3 cargoes, driving it to the vacuolar interior. In this study we have shown that the acidic di-leucine motif is indeed the sorting signal of Sna4p to the vacuolar membrane through the AP-3 dependent pathway, and that a part of Sna4p is targeted to the vacuole lumen via the multivesicular body pathway. The ability to enter multivesicular bodies is linked to the c-terminal PPPY sequence of Sna4p. Sna4p interacts with Rsp5p via this PY motif, resulting in Sna4p ubiquitylation on its lysine 128 and incorporation into the multivesicular bodies. Thus, Sna4p possesses two functional sorting signals which allow it to use two different pathways directing the protein to the vacuole.