To organize and prioritise species-specific conservation efforts, we delineate ‘functional conservation units' for the threatened Alcon Blue butterfly Maculinea alcon in Belgium. We used detailed distribution data on the butterfly, its host plant and its habitat, present-day population sizes and its mobility and colonization capacity to determine functional conservation units (FCUs) on different spatial scales: FCU-1, i.e., the 12 presently occupied habitat patches plus the area within a range of 500 m surrounding them (the maximum local movement distance, based on mark-release-recapture data), FCU-2, i.e., the areas within a range of 2 km around the occupied habitat patches (the maximum observed colonization capacity) and FCU-3, i.e., potential re-introduction sites (sites where M. alcon went extinct recently). We suggest different management and planning measures for each type of functional conservation unit and discuss translocation and re-introduction as ‘intensive care' conservation measures for this threatened and sedentary species.