Mozambique was, at the beginning of the 1900's, one of the biggest world copra producers. Since the 1990s the coconut crop became seriously threatened by Coconut Lethal Yellowing Disease (CLYD), an insect transmitted disease caused by phytoplasma, which killed, up to 2008, at least 7,000,000 coconut palms. To support the smallholder coconut sector the MCA-FISP project started in 2009 was designed to reduce the impact of the disease through the use of containment measures consisting on culling and elimination of symptomatic disease trees to reduce its spread. In the early 1980s it was estimated that Nampula and Zambezia Provinces had about 122,000 ha of coconut trees. By 2009, 40,000 ha were destroyed by the disease, with an additional 25,000 ha under heavy disease pressure. Since 2010, the FISP project hired a contractor that culled with chainsaws about 600,000 coconut trees from an area of 50,000 ha belonging to smallholder farmers. The felled palms were selected based on the visual observation CLYD symptoms. The efficiency of the selection system was further confirmed through molecular analysis showing that the level of selection mistakes was within acceptable levels. This activity effectively reduced the average disease incidence from 5% to below 2% based on annual field surveys. Because the FISP project will end by September 2013, manual tree culling by the smallholders was recently started as a strategy for sustainability which is recognized to be a reasonable solution to maintain the disease at acceptable economic levels.