<p class="MDPI17abstract"><strong>Objective: </strong>The aim of this study was to identified genetic diversity of muscovy duck in Central Java through blood protein polymorphisms by using electrophoresis method.</p><p class="MDPI17abstract"><strong>Methods: </strong>Blood sample was collected from a total of 60 muscovy ducks from the districts of Demak, Magelang and Pekalongan, 20 samples each. The Electrophoresis Polyacrylamide Gel of Electrophoresis–Thin Layer Electrophoresis (PAGE-TLE) was used in this study. Parameters observed were protein of albumin (Alb), ceruloplasmin (Cp), transferrin (Tf) and amylase-I (Am-I). Gene frequency, heterozygosity (Ho) and genetic distance were analyzed by using DISPAN program.<strong></strong></p><p class="MDPI17abstract"><strong>Results</strong><strong>: </strong>The results showed that the Alb, Cp, Tf and Am-I of muscovy duck showing polymorphic characters. Gene frequency of Alb<sup>B</sup> (0.61) was higher compared to Alb<sup>A</sup> (0.39). Gene frequency of Cp<sup>A</sup> (0.62) was higher than the Cp<sup>B</sup> (0.38). Furthermore, gene frequency of Tf<sup>A</sup> and Tf<sup>B</sup> were 0.32 and 0.68, respectively as well as gene frequency of Am-I<sup>A</sup> (0.82) was higher than Am-I<sup>B</sup> (0.18). Muscovy duck population of Demak showed higher Ho value for Alb and Am-I, whereas Magelang showed higher value for Cp and Tf. Population of muscovy duck of Demak showed closer genetic distance to Pekalongan than Magelang.<strong></strong></p><strong>Conclusions: </strong>The protein blood locus of three population of muscovy duck in Central Jawa showed polymorphic characters.