Here we report the discovery of two novel and highly divergent SHFV variants co-infecting a single male red colobus monkey (Procolobus rufomitratus tephrosceles) from Kibale National Park, Uganda. Our finding of novel, divergent SHFV variants dually infecting a wild primate sheds new light on the natural history and diversity of SHFV. In addition, using direct pyrosequencing, we were able to recover nearly complete viral genome sequences with only minimal PCR amplification. Our results therefore also confirm the authenticity of SHFV's unique genomic architecture during natural infection.