Selected wild Dahlia species in their natural habitats from west-central Mexico were tested for the presence of three caulimoviruses known to be associated with cultivated dahlia (Dahlia variabilis), viz. Dahlia mosaic virus (DMV), DMV-D10 and Dahlia common mosaic virus. Virus species-specific primers and PCR were used followed by cloning and sequencing of the amplicons. Results showed that the wild dahlia species in their natural habitat contained DMV-D10, which is an endogenous plant pararetrovirus. Viral sequences were found in 91% of the samples (n = 56) representing four different wild species. The gene coding for the movement protein of DMV-D10 from Dahlia coccinea and all other species was cloned and sequenced. Sequence comparisons showed divergence of this gene when compared to that of DMV-D10 from cultivated dahlias. The discovery of plant pararetroviruses in wild dahlia species in their natural habitats suggests a possible emergence, co-existence and co-evolution of pararetroviruses and their host plants.