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Simple Summary: The chukar partridge (Alectoris chukar) is an important bird species with significant economic and ecological value. Every year, thousands of partridges raised in Ministry of Agriculture and Forestry breeding farms are released into nature for hunting purposes. Our investigation of the gene pools of different A. chukar populations using mitochondrial and microsatellite markers from across Türkiye revealed that the Eastern, Western, and Thracian genetic structures have been shaped by Türkiye's geography and topography, past climatic fluctuations, and human-mediated artificial hybridizations. There were no signs of congeneric genetic contamination in native chukar populations, but there were contaminations with the China clade-B, which were detected as reported in the previous studies. Türkiye is considered an important evolutionary area for Chukar partridge (Alectoris chukar), since it is both a potential ancestral area and a diversification center for the species. Using 2 mitochondrial (Cty-b and D-loop) and 13 polymorphic microsatellite markers, we investigated the geographic genetic structure of A. chukar populations to determine how past climatic fluctuations and human activities have shaped the gene pool of this species in Türkiye. Our results indicate, firstly, that only A. chukar of the genus Alectoris is present in Türkiye (Anatolia and Thrace), with no natural or artificial gene flow from congenerics. Secondly, the geographic genetic structure of the species in Türkiye has been shaped by topographic heterogeneity, Pleistocene climatic fluctuations, and artificial transport by humans. Third, there appears to be three genetic clusters: Thracian, Eastern, and Western. Fourth, the post-LGM demographic expansion of the Eastern and Western populations has formed a hybrid zone in Central Anatolia (~8 kyBP). Fifth, the rate of China clade-B contamination in Türkiye is about 8% in mtDNA and about 12% in nuDNA, with the Southeastern Anatolian population having the highest contamination. Sixth, the Thracian population was the most genetically distinct, with the lowest genetic diversity and highest level of inbreeding and no China clad-B contamination. These results can contribute to the conservation regarding A. chukar populations, especially the Thracian population. [ABSTRACT FROM AUTHOR]