Andaman & Nicobar Islands (Indian Territory) are situated in the Bay of Bengal and endemic for malaria with perennial transmission. Anopheles sundaicus which prefers to breed in brackish water, is known as the main vector for malaria and maintains high endemicity of malaria. Tsunami waves entered the inhabited coastal areas, caused heavy devastation and left large areas inundated causing exceptionally high breeding sources for vector mosquitoes of malaria. The disaster created a new habitat suitable for the proliferation of malaria and other disease-carrying mosquitoes besides making thousands of people homeless. They were living in temporary open shelters, getting more exposed to mosquito bites. The population already had existing high parasite load. Hence, there was a real threat of malaria outbreak in the area. However, malaria was effectively controlled due to strategic planning and timely remedial measures. Malaria situation was monitored closely and epidemiological data of three subsequent years from 2005 to 2007 after tsunami were analysed and compared with pre-tsunami malaria data from 1986 to 2004. In this paper, effect of tsunami on malaria profile in these islands has been discussed along with action taken for its control.