A total of 80 samples were collected to analyze the mitochondrial DNA (mtDNA) and Y chromosome genetic diversity of two main Portuguese Lidia bovine populations and clarify their genetic relationships with Spanish Lidia lineages. A 521-bp D-loop fragment was sequenced in 40 animals belonging to four herds (three Brava dos Açores and one Casta Portuguesa) and the same number of samples were collected with equal distribution from males in order to genotype six microsatellites, one single

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... e polymorphism, and one indel. The mtDNA diversity recorded was similar to that observed in Lidia cattle. Haplotype T3 was the most common (62.5%), followed by the African T1 haplotype (25%); very low frequencies were recorded for haplotypes T2 (2.5%) and the Lidia haplogroup L4 (10%). The results support the existence of two major ancestral lines for the Lidia breed: European and African, similar to other Mediterranean breeds. However, the genetic diversity in the Y chromosome was lower in Portuguese Lidia lineages than in Lidia cattle and other bovine breeds (haplotype diversity = 0.09). The two major paternal haplogroups, Y1 and Y2, were present with 2.5% and 97.5%, respectively. Our results evidenced a similar paternal and maternal genetic pattern to those found in Spanish Lidia lineages and a high reproductive isolation.