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<jats:title>Abstract</jats:title><jats:p><jats:italic>Brucella melitensis</jats:italic> is a major livestock bacterial pathogen and zoonosis, causing disease and infection-related abortions in small ruminants and humans. A considerable burden to animal-based economies today, the presence of <jats:italic>Brucella</jats:italic> in Neolithic pastoral communities has been hypothesised but we lack direct genomic evidence thus far. We report a 3.45X <jats:italic>B. melitensis</jats:italic> genome preserved in an ~8000 year old sheep specimen from Menteşe Höyük, Northwest Türkiye, demonstrating that the pathogen had evolved and was circulating in Neolithic livestock. The genome is basal with respect to all known <jats:italic>B. melitensis</jats:italic> and allows the calibration of the <jats:italic>B. melitensis</jats:italic> speciation time from the primarily cattle-infecting <jats:italic>B. abortus</jats:italic> to approximately 9800 years Before Present (BP), coinciding with a period of consolidation and dispersal of livestock economies. We use the basal genome to timestamp evolutionary events in <jats:italic>B. melitensis</jats:italic>, including pseudogenization events linked to erythritol response, the supposed determinant of the pathogen’s placental tropism in goats and sheep. Our data suggest that the development of herd management and multi-species livestock economies in the 11<jats:sup>th</jats:sup>–9<jats:sup>th</jats:sup> millennium BP drove speciation and host adaptation of this zoonotic pathogen.</jats:p>