Objective A single study conducted about three decades ago on hepatitis D virus (HDV) infection among Baka pygmies in Cameroon reported a very high anti-HDV antibodies prevalence of 46%, but HDV genetic diversity has not been studied in this population. The genetic diversity of strains from endemic ancient populations may help to understand the origin and evolutionary history of viruses. This study aimed to investigate the HDV seroprevalence and the genetic diversity in three remote Cameroonian Pygmies with chronic HBV infection. Results An unusually high 69% (36/52) level of HDV infection was found among HBsAg-positive pygmies in Cameroon. HDV RNA was detected and sequenced in 38.8% (14/36). The phylogenetic analysis revealed that 9/14 strains (64.3%) were identified and classified as genotype 1 (HDV-1) and 5/14 (35.6%) as genotype 7 (HDV-7), respectively with a bootstrap value of 100%. The further analysis showed the co-circulation of highly diverse HDV genotypes HDV-1 and HDV-7 in this population. These results highlight the endemicity of HDV infection in Central Africa. The highly diverse HDV-1 and HDV-7 in pygmies suggest an African origin of HDV. However, further studies are needed with larger sample size.