Key message <p>The <i>Cmwr</i> locus was fine mapped to chromosome 2 in wrinkled-rind melon, and<i> MELO3C010304.2</i> (<i>CmNaa35</i>, encoding an<i> N</i>-α-acetyltransferase) was identified as the most likely candidate gene for wrinkled rind in melon.</p> Abstract <p>The wrinkled rind (<i>wr</i>) phenotypic trait in melon is rare, and the regulatory mechanisms and genes governing this feature remain unclear. In this study, genetic analysis of a segregating F₂ population derived from the wrinkled rind melon line T16-085 and the smooth rind line T15-022 suggested that the <i>wr</i> trait is controlled by a single recessive gene, designated <i>Cmwr</i>. Scanning electron microscopy suggested that rind wrinkling is caused by the uneven aggregation of rind cells. Bulked segregant analysis (BSA) delimited the candidate region to approximately 1.90&#xa0;Mb on chromosome 2, genetic linkage analysis refined this locus to a 448.24-kb region, and fine mapping of data from 1140 F₂ individuals restricted it to a 72.24-kb region containing eight candidate genes. The analysis of sequence variation in coding regions from the parental lines and eight melon germplasms with distinct rind morphologies indicated that <i>MELO3C010304.2</i> (annotated as an<i> N</i>-α-acetyltransferase, <i>CmNaa35</i>) was the best candidate gene for the <i>Cmwr</i> locus. Two single nucleotide polymorphism (SNP) loci in the coding region (SNP^16,734,095 and SNP^16,734,346) co-segregated with the <i>wr</i> trait. The analysis of promoter <i>cis</i>-acting elements and activity indicated that external indole-3-acetic acid treatment induced <i>CmNaa35</i> expression. Our findings suggest that <i>Cmwr</i> is responsible for the <i>wr</i> trait in melon and provide genetic resources for further investigation, including gene function analysis and the exploration of the molecular mechanisms underlying melon rind wrinkling.</p>