The genetic variation at five milk protein loci αs1-casein (CSN1S1), αs2-casein (CSN1S2), β-casein (CSN2), κ-casein (CSN3) and β-lactoglobulin (LGB) was investigated in 228 animals belonging to four dairy populations well adapted to prevailing climatic conditions of Sudan.. Bos indicus (Butana, Kenana and Baggara) and Bos indicus (Kenana or Butana) X Friesian (KBF) were studied using isoelectric focusing technique for loci characterization. All loci were polymorphic and two new variants were detected at CSN1S1 and CSN1S2. The CSN1S1*I variant was shown by the Butana and Baggara cattle, while CSN1S2*X variant was observed in all populations under the study. Milk protein loci, being positively selected loci, can also provide information about the occurrence of germplasm particularly useful for breeding strategies and production improvements.