Mobile genetic elements are also known as transposons, comprising a significant proportion of plant and animal genomes. Retrotransposons, a class of transposons, move copy and paste mechanism and, therefore, cause genome obesity. Moreover, the transferability of retrotransposons within and between different kingdoms has provided valuable information for evolutionary relationships in addition to detailed knowledge about genomes. We identified barley-specific retrotransposons (Nikita and Sukkula) and determined polymorphism ratios of these retrotransposons in a chicken genome for the first time to gain new insights for retrotransposons found in different genomes. Transposon sequences belonging to chicken and barley genomes were also investigated to understand the evolutionary relationships. For this purpose, the samples from Turkish native chicken Gerze were analyzed using a retrotransposon-based molecular marker, IRAP (inter-retrotransposon amplified polymorphism). As a result of the analyses, there was no polymorphism among the samples in Sukkula analysis, while Nikita showed 0%-60% polymorphism. Moreover, in silico analyses also presented that these two retrotransposons are closely related to other chicken retrotransposons. Obtaining results could offer a practical approach for chicken genome analyses, especially for the identification of genes to obtain desired traits.