Copy number variations (CNV) are defined as structural variation with 1 kb or larger, and are present in the genome in several forms. Gene expression and gene dosage can be affected by CNV, therefore it can be associated with diseases and livestock economic traits. Local Spanish breed such as Asturiana de los Valles (AV); Avileña Negro-Ibérica (ANI); Morucha (Mor); Pirenaica (Pi) and Retinta (Ret) breeds play an important role in the beef market in Spain. The aim of this paper was to identify CNVs being shared among the 5 breeds and verify the functional annotation of the genes within these CNVs. The 366 animals were genotyped with the Illumina BovineHD BeadChip, which 75 are from AV; 74 from ANI; 75 from Mor; 74 from Pi and 68 from Retinta. Each breed had 25 families composed by father-mother-offspring, exception those breeds that had not 75 individuals, which had 25 incomplete families (mother-offspring). The families within breed were selected to have greater genetic variability. The Penncnv software was applied to detect and filter the CNVs, which considers the BAF (B Alelle Frequency) and LRR (Log R Ratio) signals. We used the trio calling option to identify the CNVs, which consider the pedigree information after the individual CNV calling. We found CNVs being shared among breeds, varying from 87 between Pi and Ret to 514 between AV and Mor. These results suggest evidence that the formation of these breeds may be connected to common ancestry. We found the same CNV in different copy number between breeds, which means, one CNV that is a deletion in certain breed, is an insertion in another one and some of these CNVs encompassed genes. Those genes were WC1.8, PRAME, HSFY2, OAS1X, CD163L1, BOLA-DQA2, OR4P4, OR5J2, TRAC, and they are related to immune system, MHC (Major Histocompatibility Complex) and Olfactory System. Our findings speculate that some CNVs seem to be species specific and the difference of gene copy number among breeds can influence the response to environmental and pathogens challenges.