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Simple Summary: Genomic association analyses for milk yield and milk quality traits including mastitis were accomplished in a dairy cattle population from the harsh and challenging tropical savanna climate of Bengaluru, India. A further effect of selection was due to social–ecological drivers, i.e., specific constraints that are prevalent in small-sized family farms. As a time report, this study identified footprints of selection among the dairy cattle breeds in this region. The genome-wide association study (GWAS) identified two SNPs, rs109340659 and rs41571523, significantly associated with test-day milk yield. Fibrosin-like 1 (FBRSL) and calcium voltage-gated channel auxiliary subunit gamma 3 (CACN) were the respective annotated potential candidate genes. Furthermore, the genomic regions under selection were associated with pathways and mechanisms involving ubiquitination, cell signaling and immune response. Hence, contrasting dairy breeds genomically contributed to the detection of genomic regions under selection, with strong effects on adaptation and overall disease resistance. A study was designed to identify the genomic regions associated with milk production traits in a dairy cattle population reared by smallholder farmers in the harsh and challenging tropical savanna climate of Bengaluru, India. This study is a first-of-its-kind attempt to identify the selection sweeps for the dairy cattle breeds reared in such an environment. Two hundred forty lactating dairy cows reared by 68 farmers across the rural–urban transiting regions of Bengaluru were selected for this study. A genome-wide association study (GWAS) was performed to identify candidate genes for test-day milk yield, solids-not-fat (SNF), milk lactose, milk density and clinical mastitis. Furthermore, the cross-population extended haplotype homozygosity (XP-EHH) methodology was adopted to scan the dairy cattle breeds (Holstein Friesian, Jersey and Crossbred) in Bengaluru. Two SNPs, rs109340659 and rs41571523, were observed to be significantly associated with test-day milk yield. No significant SNPs were observed for the remaining production traits. The GWAS for milk lactose revealed one SNP (rs41634101) that was very close to the threshold limit, though not significant. The potential candidate genes fibrosin-like 1 (FBRSL) and calcium voltage-gated channel auxiliary subunit gamma 3 (CACN) were identified to be in close proximity to the SNP identified for test-day milk yield. These genes were observed to be associated with milk production traits based on previous reports. Furthermore, the selection signature analysis revealed a number of regions under selection for the breed-group comparisons (Crossbred-HF, Crossbred-J and HF-J). Functional analysis of these annotated genes under selection indicated pathways and mechanisms involving ubiquitination, cell signaling and immune response. These findings point towards the probable selection of dairy cows in Bengaluru for thermotolerance. [ABSTRACT FROM AUTHOR]