BACKGROUND: The impact of importation of falciparum malaria from mainland Equatorial Guinea on malaria infection in non-travellers and travellers on Bioko Island was examined. METHODS: Malaria indicator surveys were conducted in 2013 and 2014 to assess the association between malaria infection and travel to the mainland. Infection in non-travellers was compared in neighbourhoods of high travel and neighbourhoods of low travel. Boat passengers leaving from and arriving on the island were tested for infection. RESULTS: Children who had travelled to the mainland in the previous eight weeks were at greater risk of infection than those who had not travelled (56 vs 26% in 2013; 42 vs 18% in 2014). Children who had not travelled, living in localities with the highest proportion of travellers, were significantly more likely to be infected compared to those in localities with the smallest proportion of travellers (adjusted odds ratios 7.7 (95% CI 2.3-25) and 5.3 (95% CI 2.5-11) in 2013 and 2014, respectively). Infection in arriving boat passengers was substantially higher than in those departing (70 vs 38%, p = 0.017). DISCUSSION: Malaria importation by travellers poses a serious public health challenge affecting non-travellers as well as travellers.