To assess the paternal gene pool in the Lidia bovine breed (or fighting bull), a total of 603 animals belonging to 81 herds classified in 33 lineages were genotyped for six Y chromosome microsatellites, one single nucleotide polymorphism and one indel. A total of 10 haplotypes were determined with a high level of frequency variation between them, ranging from 0.2 to 74%. All the haplotypes identified belong to two previously defined major haplogroups (Y1 and Y2). Two major paternal influences were identified, corresponding to the two most common haplotypes (H1Y1 and H3Y2) with frequencies of 74 and 18%, respectively. The detection of the INRA189-104 allele evidenced an African influence in the Lidia bovine breed. Low levels of haplotype diversity have been achieved and only eight lineages showed more than one haplotype. Analysis of molecular variance showed a high level of interlineage variance (FST = 86%). Network results evidenced two main clusters made for those haplotypes belonging to Y1 and Y2 haplogroups, respectively. The findings support a high level of genetic structure together with a low level of genetic diversity in the Lidia bovine breed.