The potential applications of protein markers reveal its importance as a powerful tool in breeding improvement. Native polyacrylamide gel electrophoresis provides an accurate method for assaying variation in plasma proteins. It is a very useful technique for the detection of different genetic expressions and understanding relationship among three rabbit genotypes namely Alexandria, V-line and Baladi Black. Also, protein molecular markers can be used as linked to quantitative traits. The results of this study revealed two specific protein markers in Alexandria rabbits; these specific protein markers may be responsible for the superiority of Alexandria line at weight. Moreover, from the dendrogram, the genetic dissimilarity values were (0.11), (0.43) and (0.22) between (V & Alex), (Alex & BB), and (BB & V), respectively. Alexandria line was distinctly different from the other genotypes related in their expressions.