The wild African harlequin quails (Coturnix delegorguei delegorguei) of Western Kenya suffer from incessant hunting, habitat fragmentation, and the effects of climate change. These challenges, among others, have forced them to breed under intensive pressure, disrupting normal evolutionary processes. Here, we provide the first overview of the selection signatures in wild African harlequin quails using genotyping-by-sequencing information from 76 captured individuals. Additionally, 19 domestic Japanese quails (Coturnix coturnix japonica) were incorporated for comparative signatures of selection analysis between wild and domesticated quail species that undergo different selection pressures. Composite likelihood ratio test (CLR) and integrated haplotype score (iHS) methods were used to detect selection signatures. As a result, 252 and 424 candidate genes were detected in wild African harlequin and domestic Japanese quails, respectively, through the CLR test, whereas 150 and 457 candidate genes were identified through iHS. Some of the essential candidate genes identified in the wild African harlequin quail were associated with important traits such as immune response (MAPK13, MAPK14, CREB1, ITGB3, and PPP1CA) and morphological traits (WNT5A, GRIA1, CREB1, ADCY8, and ALK) whereas, in domestic Japanese quail, primarily production-related genes such as VIPR2, DYNLL2, COL6A3, MSX2, PRF1and GNA12 were identified. Our findings provide insights into the role of selection in shaping both wild and domestic quail genomes in terms of significant immune response, growth, reproduction, and morphological and behavioral traits.