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The honeybee, <i>Apis cerana cerana</i> (<i>Ac</i>), is an important pollinator and has adapted to the local ecological environment with relevant coloration. The cuticle coloration of the <i>brown</i> (<i>br</i>) mutant is brown instead of black in wild−type individuals. Therefore, this study aimed to identify and characterize the gene responsible for the <i>br</i> mutation. Genome resequencing with allele segregation measurement using Euclidean distance followed by Lowess regression analysis revealed that the color locus linked to the mutation was located on chromosome 11. A 2−base deletion on exon 4 was identified in the <i>g7628</i> (<i>yellow</i>) gene after genome assembly and sequence cloning. In addition, the cuticle color of the abdomen of worker bees changed from black to brown when a defect was induced in the <i>yellow</i> gene using short interfering RNA (siRNA); however, the survival rate did not decrease significantly. These results indicate that the <i>yellow</i> gene participated in the body pigmentation, and its defect was responsible for the <i>br</i> mutation. This study promotes the understanding of the molecular basis of body coloration in honeybees, enriching the molecular mechanisms underlying insect pigmentation.