The complete sequence of a watermelon-infecting Venezuelan begomovirus was obtained; it corresponds to that of the partially characterized melon chlorotic mosaic virus (MeCMV). MeCMV is a typical bipartite New World begomovirus. A putative alphasatellite, MeCMVa1, was found associated with MeCMV. This is the first satellite detected in the New World, and the first natural association of an alphasatellite with a bipartite begomovirus. The sequence of MeCMVa1 diverged highly from those of other alphasatellites, except for two atypical ones, which, like MeCMVa1, had a putative ORF2 embedded in the Rep-encoding ORF1. These findings raise new questions about the origin and evolution of subviral agents associated with begomoviruses.