Malaria was the major cause of morbidity and a leading cause of mortality in the Andaman Islands Penal Colony from 1858 to 1945. Besides annual malaria incidence peaks coinciding with the arrival of the monsoon, multi-year cycles (administrative in nature) of 10-15 years are also discernable. The size of the previous year's prisoner intake was associated (r(2)=0.21, n=57) with increased malaria. The positive relationship (r(2)=0.33, n=47) between the total number of Buddhist prisoners and malaria may have been due to prisoners of Burmese ethnicity introducing new malaria strains to the otherwise isolated islands. Well-meaning but ultimately disastrous attempts were made to drain the mangrove swamps around the penal colony. Because of the brackish-water breeding habits of the main vector, Anopheles sundaicus, engineering works along the shoreline often increased malaria. Malaria morbidity approximately trebled from 1928 to 1929 and doubled again in the next year with increases in all-cause mortality from 20/1000 in 1929 to 51/1000 in 1930, coincident with a major dredging operation for a new port. The history of malaria control in the Andaman Islands Penal Colony is a cautionary tale that well-meaning and well-funded efforts can fail spectacularly if local epidemiological reality is not well understood.