Prolactin receptor gene can influence the reproductive traits of chickens, such as broodiness and egg production. The aim of the study was to assess polymorphism and association of prolactin receptor genes with the reproductive traits of the Nigerian indigenous chicken ecotypes. A total of 100 chickens drawn from four different groups/populations of chickens were provided for the study. The chickens which comprised of laying hens only were tagged from Hen 1 to Hen 100. For further identification, hen 1 to hen 35 were tagged as population 1, and were drawn from Generation (G) 7, Heavy ecotype selected (35 hens). Hen 36 to hen 72 were tagged as population 2, and were drawn from G 8, Heavy ecotype selected (37 hens). Hen 73 to hen 90 were tagged as population 3, and were drawn from Light ecotype unselected (18 hens), and hen 91 to hen 100 were tagged as population 4, and were drawn from Heavy ecotype unselected (10 hens). Generations G7 and G8 are groups of the Nigerian heavy local chicken ecotype that have undergone seven and eight generations of selection using selection index. Two (2) blood samples were randomly collected from each population with the aid of sterile syringes and needles onto a Whatman FTA card and allowed to air dry for DNA extraction. The DNA was extracted using the GenoAid extraction protocol. PCR was conducted and the product was then viewed on 2% agarose gel. The sequence results showed that a total of 206 base pairs (bp) screened for prolactin receptor PRLR5a gene did not have any polymorphism across the samples studied. However, on prolactin receptor PRLR6 gene, 195 base pairs were screened and variation occurred at polymorphic site 47bp with nucleotide base “A” transcribed to “G”, and the possible genotypes were “AG” and “GG”. The phylogenetic tree analysis clustered the samples into two branches and showed that individuals with “GG” genotype performed better than those birds with AG genotype in the reproductive traits considered. It was therefore, concluded that prolactin receptor PRLR6 gene was polymorphic at site 47 bp and positively associated with the reproductive traits: body weight at first egg, body weight at 16th week of egg production, total egg number and average egg weight. The mutated genotype (GG) showed superior performance over the normal genotype (AG) of the Nigerian indigenous chicken ecotypes.