In the Iberian Peninsula, populations of two subspecies of the Reed Bunting Emberiza schoeniclus have become increasingly fragmented during the last decades when suitable habitats have been lost and/or the popula- tions have gone extinct. Presently, both subspecies are endangered. We estimated the amount of genetic variation and population structure in order to define conservation units and management practices for these populations. We found that the subspecies lusitanica has clearly reduced genetic variation in nuclear and mitochondrial markers, has a drastically small effective population size and no genetic differentiation between populations. In contrast, the sub- species witherbyi is significantly structured, but the popu- lations still hold large amounts of variation even though the effective population sizes are smaller than in the non- endangered subspecies schoeniclus. We suggest several management units for the Iberian populations. One unit includes subspecies lusitanica as a whole; the other three units are based on genetically differentiated populations of witherbyi. The most important genetic conservation mea- sure in the case of lusitanica is to preserve the remaining habitats in order to at least maintain the present levels of gene flow. In the case of the three management units within witherbyi, the most urgent conservation measure is to improve the habitat quality to increase the population sizes.