Characterization and genetic diversities among members of a species are fundamental to their improvement and conservation. This study was conducted to characterize and estimate genetic diversity in the ecotypes of the locally adapted Muscovy duck in Nigeria using blood proteins (haemoglobin, transferrin and albumin) and enzyme (carbonic anhydrase) markers. Blood samples collected from 20, 40 and 20 adult Muscovy ducks sampled randomly from the Rain Forest, Derived Savanna and Guinea Savanna ecotypes, respectively, were typed for blood proteins and enzyme polymorphism with cellulose acetate paper. Genetic variability in the studied population was accessed using heterozygosity (H), effective number of allele (ne) and polymorphism (percent P). All the 13 allelic variants expressed at the four loci were expressed in the Derived Savanna ecotype but 12 each in the Rain Forest and Guinea Savanna ecotypes. Results showed that all the four loci were polymorphic (100 percent) and the estimated heterozygosity among them was similar (0.424–0.481). Similarity in the estimated genetic variability parameters among ecotypes indicate that the sub-populations understudy was under similar evolutionary forces and there were no appreciable differences among them.