Studies of population structure and diversity in cattle have provided insights into the origins of breeds, their history and evolution, and allow the identification of global livestock diversity hotspots, which is important for conservation of diversity. Genetic diversity, genetic relationship, population structure, and the presence of hotspots of genetic diversity among 15 European bovine breeds from five countries were assessed using 435 single nucleotide polymorphisms (SNP) markers identified in candidate genes for muscle, lipid and energy metabolism, thus providing the opportunity to compare the breed relationships obtained using putatively functional markers with previous data using neutral loci. Individuals belonging to 11 breeds tended to be clearly assigned to a single cluster when the number of pre-defined populations reached a maximum in the likelihood of the data at K= 12, whereas Asturiana de los Valles, Danish Red, Simmental, and Avileña-Negra Ibérica displayed a greater degree of admixture, which may be explained by their diverse ancestry. Although overall results were in agreement with those reported by studies based on neutral genetic variations, some additional breed relationship information emerged using markers in candidate functional loci, including the relationship between the Asturiana de los Valles and Piedmontese, and Danish Red and Charolais breeds. This study indicates that the analysed loci have not been main targets for selection or for adaptation processes, but also that SNP within candidate genes related with beef characteristics and performance may provide a slightly new perspective on past breeding and may also help in the development of strategies for the rational conservation of livestock diversity.