To confirm the local endemicity of Schistosoma haematobium on Mafia Island, Tanzania, conjoint parasitological and malacological surveys were undertaken in July 2006 with parasitological investigations supplemented with case-history questionnaires. A total of 238 children (125 girls and 113 boys, mean age of 13.9 years) across 9 primary schools were examined. The prevalence of micro-haematuria and egg-patent infection was 18.1% (CI95=9.6-33.6) and 4.2% (CI95=1.9-7.6), respectively but a strong female bias was observed for micro-haematuria (5.6F:1M) contrasting with a strong male bias for the presence of eggs (1F:4M). All egg-patent infections were of light-intensity (<10eggs/10ml). No clear associations between infection prevalence and local water-contact, by school, were found and all 10 of the egg-positive children had a travel history to the nearby mainland or Zanzibar. Inspection of community diagnostic registers at Kilindoni Hospital revealed a low proportion (<2%) of egg-patent infection for 20,306 samples tested in the 2000-2005 period. A total of 43 freshwater sites, a third of which were previously sampled in 1999 and 2002, were surveyed and 11 species of freshwater mollusc were found. Four species of Bulinus (B. nasutus, B. forskalii, B. barthi and B. sp.) were encountered across 13 sites with B. nasutus restricted to 3 of these towards the north of the island. No collected snail was observed to shed schistosome cercariae. Further characterisation of B. nasutus and S. haematobium included infection challenge on two occasions, with miracidia obtained from egg-patent children from Mafia and Unguja islands as well as DNA barcoding of snails and schistosomes. B. nasutus was shown refractory to infection. With the substantial travel to and from Mafia, the refractory nature of local snails and evidence from DNA barcoding in schistosomes and snails, we conclude that urogenital schistosomiasis is an imported infection.