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• A map of Copy Number Variants in Mexican Creole Cattle obtained with the Illumina 7,77,000 BovineHD BeadChip. • CNVs genomic clustering of individual occurred according to their geographical origins. • Genes enriched in CNVRs are mainly involved in immune response and inflammation. Mexican Creole Cattle (MCC) derived from cattle of the Iberian Peninsula, mainly from Andalucía and Extremadura, and were introduced in central America the 16th century. Copy Number Variants (CNVs) are structural variants contributing to the genetic diversity among populations and related to variation in phenotypic expression. More than half of the identified CNVs regions in human and livestock include protein-coding genes involved in essential function, as cellular functionality, metabolic pathways and disease susceptibility. The aim of this study is to investigate the CNVs genomic variation in the MCC population. A total of 48 unrelated individuals (5 males and 43 females) were genotyped with the BovineHD Genotyping BeadChip Illumina, containing 7,77,962 polymorphic SNPs. A total of 2170 CNVs were detected in 40 individuals, summarized into 733 CNV regions, covering 32.1 Mb of the bovine autosome genome. Functional analysis of the CNVRs identified 131 genes mainly involved in immune response and inflammation, and 923 overlapping QTL classified in six difference QTL-term categories. Cluster and PCA analyses showed a samples distribution in concordance with the geographical origins of the sub-populations, highlighting both a sharing genetic background together with a diversification of populations as a response to adaptation to different and adverse environments. [ABSTRACT FROM AUTHOR]