The most representative sheep in Sicily are Belicina, Comisana, Pinzirita, Barbarescaand the crossbred derived sheep from all this species. In this study, the allelic frequencies of the Sicilian sheep population were investigated. It currently represents the best way to determine the genetic identity and/or family even with limited amounts of sample or when the DNA is degraded. The aim of the study was to provide a reference data bank and to evaluate a microsatellite panel for pedigree analysis as suggested by the International Society for Animal Genetics (ISAG). There are various studies on European sheep, but few datasets were developed on the population of Sicilian sheep. The reference database will include allele frequencies at each locus and will determine genetic parameters for Sicilian ovine species selection. Our results indicated that Hardy Weinberg equilibrium was not always maintained. These results could be explained by a non-random mating. The database is useful to investigate the relationship, the parentage the meat traceability and in disease control programs. The standardized panels of allele frequencies represent a molecular fingerprinting characterizing the subjects with very high definition level and can be useful to control all the livestock. The parentage identification could be important for the veterinary police to investigate the theft or the animal substitutions in the Sicilian farms