Although the small Arf-like GTPases Arl1-3 are highly conserved eukaryotic proteins, they remain relatively poorly characterized. The yeast and mammalian Arl1 proteins bind to the Golgi complex, where they recruit specific structural proteins such as Golgins. Yeast Arl1p directly interacts with Mon2p/Ysl2p, a protein that displays some sequence homology to the large Sec7 guanine exchange factors (GEFs) of Arf1. Mon2p also binds the putative aminophospholipid translocase (APT) Neo1p, which performs essential function(s) in membrane trafficking. Our detailed analysis reveals that Mon2p contains six distinct amino acid regions (A to F) that are conserved in several other uncharacterized homologs in higher eukaryotes. As the conserved A, E and F domains are unique to these homologues, they represent the signature of a new protein family. To investigate the role of these domains, we made a series of N- and C-terminal deletions of Mon2p. Although fluorescence and biochemical studies showed that the B and C domains (also present in the large Sec7 GEFs) predominantly mediate interaction with Golgi/endosomal membranes, growth complementation studies revealed that the C-terminal F domain is essential for the activity of Mon2p, indicating that Mon2p might also function independently of Arl1p. We provide evidence that Mon2p is required for efficient recycling from endosomes to the late Golgi. Intriguingly, although transport of CPY to the vacuole was nearly normal in the Δmon2 strain, we found the constitutive delivery of Aminopeptidase 1 from the cytosol to the vacuole to be almost completely blocked. Finally, we show that Mon2p exhibits genetic and physical interactions with Dop1p, a protein with a putative function in cell polarity. We propose that Mon2p is a scaffold protein with novel conserved domains, and is involved in multiple aspects of endomembrane trafficking.