There is a significant and steadily growing market for breeding falcons, including all hybrids. The increased demand cannot be met exclusively through the legal market. Due to the free flying period of the bred animals and a loss rate of 10%, hybrids in particular pose a significant threat of introducing undesirable genes into local wild populations. Therefore, there is a high interest in methods for identification not only of hybrids but also for genetic characterization of pure falcon species. To address this question in the present study, 869 falcons from three different falcon species and four different breeders were genotyped using 14 microsatellites (fp5, fp13, fp31, fp46-1, fp54, fp79-1, fp79-4, fp82-2, fp86-2, fp89, fp92-1, fp107, fp347, and fr34). Nuclear DNA was amplified by PCR and separated by gel electrophoresis. The results were analyzed population genetically and statistically. The present study provides for the first time an overview of the genetic structure of four European falcon breeders. The fact that 114 hybrid animals were found among the avoidably pure animals is one of the most important results of the study. Due to an unexpectedly high genetic similarity between the studied falcons, no absolute differentiation or identification of all individuals could be achieved with the available microsatellite set in 11 pairs of individuals. Thus, further research is needed to establish gene markers with higher informativeness. One reason for the high agreement of the animals is the presumably high rate of full siblings among the sent samples, which could not be clarified conclusively, because the samples were not accompanied by pedigrees. However, the fact that 50 % of the individuals showed an allele match between 50 and 79 %, the high occurrence of major alleles, the many monomorphic loci and the high homozygosity levels speak for the actually high genetic concordance of the animals. However, the major alleles affect the population genetic parameters as well as all calculations based on the Hardy-Weinberg equilibrium. Furthermore, it remains to be considered that only the populations Z2G, Z3G, Z4G, Z2S and Z2W have a sufficiently high population size to perform an evaluation of the population genetic parameters. In four cases, physical linkages resulted between markers (locus: fp86-2 and fp54; fp82-2 and fp347; fp82-2 and 31; and fp347 and fp31) and 236 of the 809 comparisons showed significant linkage disequilibrium. The linkages were spurious linkages because the markers were either physically separated by several million base pairs, so recombination could be assumed, or comparable studies failed to detect linkages. Furthermore, the linkage disequilibrium frequencies can be explained by the high levels of homozygosity and by unintentional mixing of individuals from subpopulations (Wahlund effect). The FST values as well as the many heterozygote deficits (populations Z2G, Z3G, Z4G) indicate a Wahlund effect. Although all microsatellites were used in the comparative studies and were also established in this study, the occurrence of null alleles could not be completely excluded. There were 15 cases of "true" null alleles at microsatellite fp54 and six allelic dropouts (significantly increased null allele frequency) at locus MSFp01, four at locus fp54, and three at locus fp92-1. In 14 of the 15 cases showing increased null allele frequency, a significant heterozygote deficit could be detected. Therefore, heterozygote deficits rather than null alleles are assumed to be the cause of the deviations from Hardy-Weinberg equilibrium. An examination of the ger, saker and peregrine falcon populations showed no genetic differentiation between ger and saker falcons. Only a second hierarchical cluster analysis (by the computer program Structure) was able to differentiate these species. Only on the basis of Nei genetic distance and by a discriminant analysis of principal components (DAPC) the populations subdivided analogously to the species partition. By an analysis of molecular variance (AMOVA) the individual populations could be represented. Furthermore, the results of the present study were compared with eight comparative studies on European peregrine, gyr and saker falcon. In summary, the range of values for population genetic indices was similar for both wild and breeding populations. This resulted in only minor differences for genetic variability between wild and breeding populations. This is because most studies sampled populations after the population decline in the 1970s and these populations already showed lower levels of genetic variation. This is also indicated by the extremely high number of monomorphic loci, low allelic richness values, monomorphic loci, and low effective allele counts in the present study. The comparative studies showed fewer major alleles than the present study, also emphasizing the lower genetic diversity. It is notable here that the affected alleles are the same loci as in the present study. This is also corroborated by the lower values for expected (He) and observed heterozygosity (Ho). The results of the present study indicate inbreeding due to the low allele numbers, trend towards major alleles, many monomorphic loci, reduced linkage disequilibrium, significant heterozygote deficiencies, positive FIS values, AMOVA results, paired genetically identical individuals (IPs), low effective population sizes and values for effective allele number, and low values of He and Ho. Even exchange of individuals between breeders is likely to improve this situation only partially, because the genetic distances between the different breeding populations are also small. For an improved breeding strategy, to minimize inbreeding, to increase genetic diversity and to clarify whether breeding falcons are hybrids, it is recommended that breeders investigate the genetic status of their falcon populations and, based on this, make targeted pairing of breeding animals with the most pronounced genetic distance possible.