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<i>MdPG1</i> encoding polygalacturonase in apple (<i>Malus</i> × <i>domestica</i>) is a key gene associated with fruit firmness and texture variations among apple cultivars. However, the causative variants of <i>MdPG1</i> are still not known. In this study, we identified a SNP^A/C variant within an ERF-binding element located in the promoter region of <i>MdPG1</i>. The promoter containing the ERF-binding element with SNP^A, rather than the SNP^C, could be strongly bound and activated by MdCBF2, a member of the AP2/ERF transcription factor family, as determined by yeast-one-hybrid and dual-luciferase reporter assays. We also demonstrated that the presence of a novel long non-coding RNA, <i>lncRNA_PG1</i>, in the promoter of <i>MdPG1</i> was a causative variant. <i>lncRNA_PG1</i> was specifically expressed in fruit tissues postharvest. <i>lncRNA_PG1</i> could reduce promoter activity when it was fused to the promoter of <i>MdPG1</i> and a tobacco gene encoding Mg-chelatase H subunit (<i>NtCHLH</i>) in transgenic tobacco cells but could not reduce promoter activity when it was supplied in a separate gene construct, indicating a <i>cis</i>-regulatory effect. Our results provide new insights into genetic regulation of <i>MdPG1</i> allele expression and are also useful for the development of elite apple cultivars.