It is generally believed that hepatitis B (HBV) and C (HCV) viruses are highly prevalent in the Republic of Yemen. This study investigated the prevalence of HBV and HCV markers in 494 blood donors from Aden, 493 blood donors from Sana'a, 97 residents from an African ethnic minority in Sana'a and 99 residents of Soqotra Island. There were significant differences in the prevalence of HBV carriage (HBsAg: 6·7, 15, 19·6 and 26·3% respectively; P<0·001); past HBV infection (anti-HBc: 17·4, 18·5, 30·9 and 59·6% respectively; P<0·001); susceptibility to HBV (absence of HBV markers: 73·3, 61·9, 38·1 and 9·1% respectively; P<0·001), infectivity of HBV carriers (HBV DNA: 51·5, 33·8, 52·6 and 65·4% respectively; P=0·028) and HCV antibodies (RIBA confirmed or indeterminate: 0·6, 0·2, 5·2 and 5·1% respectively; P<0·001). A significant difference in HBV carrier rate and a borderline significant difference in the prevalence of natural infection was observed between males and females in the African community (P=0·02 and 0·06 respectively). In contrast, in Soqotra Island, there was no significant sex difference in HBV carrier rate but susceptibility was significantly more prevalent in males (P=0·03). This study illustrates that significant difference in prevalence and epidemiology exists among different communities within the same country, reflecting political, geographical and social differences. Control strategies should take these differences into account.