Understanding connectivity among populations in fragmented landscapes is of paramount importance in species conservation because it determines their long-term viability and helps to identify and prioritize populations to conserve. Rare and sedentary species are particularly vulnerable to habitat fragmentation as they occupy narrow niches or restricted habitat ranges. Here, we assess contemporary interpopulation connectedness of the threatened, myrmecophilous butterfly, Maculinea alcon, in a highly fragmented landscape. We inferred dispersal, effective population sizes, genetic diversity and structure based on 14 locations of M. alcon in Belgium and the Netherlands using data from 12 microsatellite loci. Despite the reported sedentary behaviour of M. alcon, we observed moderate levels of contemporary dispersal between patches, but only in landscapes where populations were located within a distance of 3 km from neighbouring populations. Estimates of effective population sizes (Ne) were very low (ranging from 1.6 to 17.6) and bottleneck events occurred in most of the studied populations. We discuss the functional conservation units delineated based on a former mark-release-recapture study, and formulate appropriate conservation strategies to maintain viable (meta)populations in highly fragmented, anthropogenic landscapes.