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Semi-feral local livestock populations, like Maremmana cattle, are the object of renewed interest for the conservation of biological diversity and the preservation and exploitation of unique and potentially relevant genetic material. The aim of this study was to estimate genetic diversity parameters in semi-feral Maremmana cattle using both pedigree- and genomic-based approaches (<inline-formula><math display="inline"><semantics><msub><mi>F</mi><mrow><mi>I</mi><mi>S</mi></mrow></msub></semantics></math></inline-formula> and <inline-formula><math display="inline"><semantics><msub><mi>F</mi><mrow><mi>R</mi><mi>O</mi><mi>H</mi></mrow></msub></semantics></math></inline-formula>), and to detect regions of homozygosity (ROH) and heterozygosity (ROHet) in the genome. The average heterozygosity estimates were in the range reported for other cattle breeds (<inline-formula><math display="inline"><semantics><mrow><msub><mi>H</mi><mi>E</mi></msub><mo>=</mo><mn>0.261</mn></mrow></semantics></math></inline-formula>, <inline-formula><math display="inline"><semantics><mrow><msub><mi>H</mi><mi>O</mi></msub><mo>=</mo><mn>0.274</mn></mrow></semantics></math></inline-formula>). Pedigree-based average inbreeding (<i>F</i>) was estimated at <inline-formula><math display="inline"><semantics><mrow><mn>4.9</mn><mo>%</mo></mrow></semantics></math></inline-formula>. The correlation was low between <i>F</i> and genomic-based approaches (<inline-formula><math display="inline"><semantics><mrow><mi>r</mi><mo>=</mo><mn>0.03</mn></mrow></semantics></math></inline-formula> with <inline-formula><math display="inline"><semantics><msub><mi>F</mi><mrow><mi>I</mi><mi>S</mi></mrow></msub></semantics></math></inline-formula>, <inline-formula><math display="inline"><semantics><mrow><mi>r</mi><mo>=</mo><mn>0.21</mn></mrow></semantics></math></inline-formula> with <inline-formula><math display="inline"><semantics><msub><mi>F</mi><mrow><mi>R</mi><mi>O</mi><mi>H</mi></mrow></msub></semantics></math></inline-formula>), while it was higher between <inline-formula><math display="inline"><semantics><msub><mi>F</mi><mrow><mi>I</mi><mi>S</mi></mrow></msub></semantics></math></inline-formula> and <inline-formula><math display="inline"><semantics><msub><mi>F</mi><mrow><mi>R</mi><mi>O</mi><mi>H</mi></mrow></msub></semantics></math></inline-formula> (<inline-formula><math display="inline"><semantics><mrow><mi>r</mi><mo>=</mo><mn>0.78</mn></mrow></semantics></math></inline-formula>). The low correlation between <i>F</i> and <inline-formula><math display="inline"><semantics><msub><mi>F</mi><mrow><mi>R</mi><mi>O</mi><mi>H</mi></mrow></msub></semantics></math></inline-formula> coefficients may be the result of the limited pedigree depth available for the animals involved in this study. The ROH islands identified in Maremmana cattle included candidate genes associated with climate adaptation, carcass traits or the regulation of body weight, fat and energy metabolism. The ROHet islands contained candidate genes associated with nematode resistance and reproduction traits in livestock. The results of this study confirm that genome-based measures like <inline-formula><math display="inline"><semantics><msub><mi>F</mi><mrow><mi>R</mi><mi>O</mi><mi>H</mi></mrow></msub></semantics></math></inline-formula> may be useful estimators of individual autozygosity, and may provide insights on pedigree-based inbreeding estimates in cases when animals’ pedigree data are unavailable, thus providing a more detailed picture of the genetic diversity.