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Background: The Comoros are an archipelago located in the Indian Ocean between the eastern coasts of Africa and north of Madagascar. Malaria transmission appeared late in the 19th century due to the intensification of human migration. The story of malaria transmission for the past century is depicted to provide useful lessons for the future. Currently, malaria transmission occurs differently on each island; thus, control strategies must be adapted for each particular island. Tentative malaria control in Comoros has a long history of success and failure. This study reviews the data available as a basis for recommendations for the future., Results: There has been much effort to reach a pre-eradication state in Anjouan and Moheli, but only control steps have been taken in the Great Comoro. To date, the primary strategy used is mass treatment of the population using artemisinin-based combination therapy (ACT), which is similar to the strategy deployed during the 1950s in other countries. ACT appears efficient in two of the three islands; however, the sustainability of the strategy is unknown. This sustainability is compromised by (i) the huge level of uncontrolled exchange between the Comoro Islands and their neighbours, increasing the risk of introducing ACT-resistant strains, (ii) the use of large quantities of pesticides for agriculture usually associated with the resistance of mosquitoes, and (iii) the cost of the actions themselves., Conclusions: In view of the history of malaria in this area, the first recommendation is to enhance the training of health workers and the population. The second step is to establish a national strategy to assess malaria and related factors, which is currently lacking. A survey to assess the drug sensitivity of the parasites is particularly important in a context of low transmission associated with mass treatment of the population. The last point should be to secure financial support, which is not obvious in a context of pre-elimination. The Comoro Islands are thus a living laboratory to experiments with strategies for elimination, but the future is complex.