Abstract A purpose of this study was to evaluate genetic diversity in duck populations based on polymorphic variants (H1.a, H1.b and H1.z) of linker histone H1. The study was performed using conservative brown-feathered Khaki Campbell (Kh1) and Orpington (Or) populations and white-feathered Pekin (P77) duck breeding line. While no significant distortion between both brown-feathered duck populations was noted (P>0.05), the allele frequencies at histone H1 polymorphic loci were found to differ significantly between brown-feathered and white-feathered duck flocks (P<0.001). While the alleles a1, b1 and z1 were detected in all three duck lines, the alleles a2 and b2 missed in the line P77 were found in the Kh1 and Or populations. A rare allele z2 not detected in a homozygous state during screening our duck populations was found to occur only in heterozygous P77 duck individuals (z1z2). After a purpose mating of these heterozygous P77 birds, the homozygous individuals (z2) were obtained in their offspring. The uneven distribution of the alleles for polymorphic histone H1 variants among duck populations seems to suggest that they are not functionally equivalent and, therefore, might have a differential influence on chromatin structure and/or function leading to line-specific phenotypic effects in duck.