This study investigates the genetic relationships and heterozygosity-rich regions (HRR) in 30 Italian and 19 worldwide goat breeds using the Illumina GoatSNP50k BeadChip. The research aims to understand inter-breed relationships and HRR patterns using sliding window (SW) and consecutive runs (CR) detection methods. Genetic diversity indices revealed a clear separation between non-European and European breeds, with European breeds showing higher heterozygosity and lower inbreeding. The Pearson correlation coefficients between HRR parameters obtained from SW and CR methods were high, indicating consistent results. A total of 166 HRR islands were identified, with chromosomes CHI3, CHI11, CHI12, and CHI18 harboring the highest number of islands. Genes within these islands are linked to various functional traits such as productivity, reproduction, and immune response. The Montecristo feral goat, despite high inbreeding, showed the highest number of HRR islands, suggesting potential balancing selection events. The study highlights the importance of species-specific HRR patterns in understanding genome modeling and evolutionary history.This study investigates the genetic relationships and heterozygosity-rich regions (HRR) in 30 Italian and 19 worldwide goat breeds using the Illumina GoatSNP50k BeadChip. The research aims to understand inter-breed relationships and HRR patterns using sliding window (SW) and consecutive runs (CR) detection methods. Genetic diversity indices revealed a clear separation between non-European and European breeds, with European breeds showing higher heterozygosity and lower inbreeding. The Pearson correlation coefficients between HRR parameters obtained from SW and CR methods were high, indicating consistent results. A total of 166 HRR islands were identified, with chromosomes CHI3, CHI11, CHI12, and CHI18 harboring the highest number of islands. Genes within these islands are linked to various functional traits such as productivity, reproduction, and immune response. The Montecristo feral goat, despite high inbreeding, showed the highest number of HRR islands, suggesting potential balancing selection events. The study highlights the importance of species-specific HRR patterns in understanding genome modeling and evolutionary history.