The Centaurea parlatoris group belongs to sect. Dissectae and is one of the most taxonomically critical groups in Sicily. The taxa included in it inhabit dry slopes, pastures and rocky places. Some of them are narrow endemics to Sicily, and others to Italy. The great morphological variability at the intrapopulation level has not permitted the creation of an adequate taxonomic scheme. The recent proposal of two new species from Sicily confirms the insufficient knowledge of the taxonomic diversity. This study involves eight Sicilian populations of the C. parlatoris group. Seven loci from nine enzyme systems [isocitrate dehydrogenase (IDH), malate dehydrogenase (MDH), 6-phosphogluconate dehydrogenase (6-PGD), phosphoglucomutase (PGM), alcohol deydrogenase (ADH), shikimate deydrogenase (SKD), leucine aminopeptidase (LAP), glutamate-oxaloacetate transaminase (GOT) and phosphoglucoisomerase (PGI)] were examined. A total of 23 alleles were identified; seven were fixed in different populations, others were rare. The allele frequencies and the genetic variability values for each population were calculated. The highest intrapopulation variability was found in the populations of Monte Occhio and San Martino (71.4%), as well as in C. giardinae and C. sicana (57.1%). The lowest values were registered in the population of Isnello. The obtained dendrogram reflects the recent taxonomic treatment of the group. The study can provide means for both assessment of the future impact of erosion on diversity and elaboration of effective conservation strategies for these endemic taxa.