The genetic associations and differences of four protein fractions were investigated in Tibetan wild barley. Albumin, globulin and hordein contents were under genetic control probably via multiple genes/quantitative trait loci. A correlation analysis showed that globulin was significantly associated with albumin, glutelin and hordein, while hordein was closely correlated with glutelin. Forty-nine diversity array technology (DArT) markers, which were distributed over seven chromosomes, were associated with the protein fraction contents. Those DArT markers associated with hordein were the same as those associated with globulin and glutelin. Only five markers associated with hordein, globulin and glutelin were also associated with albumin. Most of the protein fraction contents are therefore controlled by same genes which may contribute to total protein content. The discovery of new markers associated with specific protein fractions could be used to detect genes controlling protein content in the barley germplasm.