We carried out a comprehensive genomic analysis of porcine copy number variants (CNVs) based on whole-genome SNP genotyping data and provided new measures of genomic diversity (number, length and distribution of CNV events) for a highly inbred strain (the Guadyerbas strain). This strain represents one of the most ancient surviving populations of the Iberian breed, and it is currently in serious danger of extinction. CNV detection was conducted on the complete Guadyerbas population, adjusted for genomic waves, and used strict quality criteria, pedigree information and the latest porcine genome annotation. The analysis led to the detection of 65 CNV regions (CNVRs). These regions cover 0.33% of the autosomal genome of this particular strain. Twenty-nine of these CNVRs were identified here for the first time. The relatively low number of detected CNVRs is in line with the low variability and high inbreeding estimated previously for this Iberian strain using pedigree, microsatellite or SNP data. A comparison across different porcine studies has revealed that more than half of these regions overlap with previously identified CNVRs or multicopy regions. Also, a preliminary analysis of CNV detection using whole-genome sequence data for four Guadyerbas pigs showed overlapping for 16 of the CNVRs, supporting their reliability. Some of the identified CNVRs contain relevant functional genes (e.g., the SCD and USP15 genes), which are worth being further investigated because of their importance in determining the quality of Iberian pig products. The CNVR data generated could be useful for improving the porcine genome annotation.