Wool properties and commodity value vary considerably between breeds. In Portugal, three major ovine groups exist: Churros, Bordaleiros and Merinos. This work studies the effect of the ovine genotype on the wool proteome of such groups. Wool was collected from 15 ewes/breed and genetic groups: Churra da Terra Quente (CTQ) or Churro, Serra da Estrela (SE) or Bordaleiro and Merino Branco (MB) or Merino. Proteins were extracted and subjected to label-free proteomics analysis. A total of 50 keratinous protein groups were identified in all the samples, divided into type I and II keratins and the keratin associated proteins: high-glycine-tyrosine proteins, ultra-high sulphur proteins and high-sulphur proteins. Major differences were found between MB and CTQ with respect to K75 and K38, both medullar proteins and to a lesser extent between SE and CTQ suggesting that these might be good markers for this trait in wool. Partial least squares discriminatory analysis proved MB to be readily distinguishable from the other two breeds. Further differences were noted in keratin associated protein levels between the three breeds, normally an indicator of higher levels of orthocortex and also their relationship to high curvature, high crimp fibres like Merino. Biological significanceThe ovine genetic type has strong effects on wool productivity parameters and quality traits. In this work, we compare the proteomes and the microscopical characteristics of the wool from three distinct ovine genetic types from Portugal: Merino, Bordaleiro and Churro. Important differences were found regarding keratin associated proteins and keratins K75 and K38, suggested as putative markers for quality traits in the wool proteome such as the average curvature.