Rhynchosia minima is a host for several begomoviruses, both in the Old World and the New World. In Cuba, a whitefly-transmitted disease causing yellow mosaic symptoms, suggested to be of viral origin, was described more than 30 years ago in R. minima, but no information about the nature of the viruses infecting this weed in this country is available to date. Here, we report the detection of isolates of two novel begomovirus species infecting R. minima in Cuba, which we proposed be named Rhynchosia golden mosaic Havana virus (RhGMHaV) and Rhynchosia rugose golden mosaic virus (RhRGMV). The highest nucleotide sequence identities of RhGMHaV and RhRGMV DNA-A were with isolates of Rhynchosia golden mosaic virus (78.7%) and Sida golden mosaic virus (87.5%), respectively. Phylogenetic analysis demonstrated that these novel viruses belong to two different lineages of New World begomoviruses.