Plumage color is one of the key phenotypic traits for breed identification in poultry, and deciphering its genetic basis is of great significance for the conservation and sustainable utilization of germplasm resources. In this study, we performed whole-genome sequencing (WGS) on 127 Guangdong Black pigeons and 12 Tarim pigeons, and integrated existing WGS data from four other pigeon breeds (40 individuals in total). Principal component analysis, population structure analysis, and phylogenetic tree construction revealed that Guangdong Black pigeons have a unique genetic background and are clearly differentiated from white- and gray-feathered pigeon populations. We further conducted a genome-wide association study (GWAS), and after filtering and screening, identified a total of 1,598 single-nucleotide polymorphisms (SNPs) and 97 insertions/deletions (InDel). These loci were predominantly clustered in the endothelin receptor type B2 (EDNRB2) gene on chromosome 4 and in its flanking regions. From this region, we selected three highly significant SNPs and two InDels for Sanger sequencing validation. The results showed that all tested loci in white-feathered pigeons were wild-type, whereas in Guangdong Black pigeons they were either homozygous mutant or heterozygous, indicating that the genotypes at these variant loci are highly consistent with the black plumage phenotype. Our results provide reliable candidate markers for elucidating the molecular mechanism underlying plumage color formation in Guangdong Black pigeons and for implementing molecular marker-assisted breeding.