The taxonomic status of Alcon Blues in Central and Western Europe (conventionally: Maculinea alcon and M. rebeli) is confused. Some authors distinguish them as separate species within the M. alcon species group, while others consider them to be subspecies or simply ecological forms. Our aim was to study the geographical versus food plant pattern of genetic differentiation among several populations of these taxa in Northern Hungary. Imagines were collected from 11 localities between 2000 and 2003. M. alcon feeding on G. pneumonanthe from three subregions and on G. cruciata from two subregions were analysed. Enzyme polymorphism was analysed at 16 enzyme loci using polyacrylamide gel electrophoresis. In the analysis of the data, F-statistics were computed and the total genetic variation partitioned into within and between population components. Nei's genetic distances were calculated and a UPGMA dendrogram constructed on the basis of the distance matrix. Hierarchical F-statistics and AMOVA were computed to study the pattern of genetic differentiation among the samples. PCA analysis was also carried out using the allele frequencies of the samples. The results of all analyses indicated strong differentiation among the samples. A sizeable portion of this variation was detected among the samples/generations collected from the same population. The distribution of the between population variation did not exhibit a clear split between the two food plant groups. In addition, the FST values computed using a restricted data set suggested significant differentiation among the subregions. The results of AMOVA and PCA also indicated that the geographic pattern was more expressed in the between sample variation than the conventional taxonomic pattern.