Using direct pyrosequencing, we have demonstrated infection of a male red colobus monkey from Kibale National Park, Uganda, with two novel SHFV variants. To our knowledge, this is the first report of SHFV in a wild primate. These new viruses, SHFV-krc1 and SHFV-krc2, are highly divergent from each other and from the type strain (approximately 52% nucleotide sequence identity among the three variants). Both new viruses nevertheless contain homologs of the type strain SHFV ORFs 2a, 2b, and 3 in the same genomic positions.