The family Geminiviridae comprises seven genera differentiated by genome organisation, sequence similarity and insect vector. Metagenomics-based studies conducted in Europe, Asia and Africa between 2010 and 2011 have yielded a 8th novel genus, the so-called Capulavirus genus, from which two species (Euphorbia caput-medusae latent virus, EcmLV; and Alflafa leaf curl virus, ALCV) were recently fully characterized. These metagenomics-based studies were conducted in both the Western Cape region of South Africa and the Rhône delta river region of France. Spatial and host distributions of height novel geminiviruses, including EcmLV and ALCV were determined. We here present the full characterization of a novel geminivirus isolated from a South African endemic plant (Polygala garcinii DC). Seven full genomes of this novel geminivirus were obtained from a collection of 34 plants collected in 2012 and 2015. While the whole genome phylogenetic trees indicate that this new geminivirus isolates cluster with the other described begomoviruses isolates, it is apparent from the CP phylogenetic tree that CP protein sequences of this new geminivirus are slightly divergent from all currently known begomovirus CP protein sequences.