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• 'Huarongdao Zhoupigan' is a cultivated landrace with a history of more than a hundred years. • Parentage and origination was predicted by morphological, SSR marker and genomic analyses. • 'Huarongdao Zhoupigan' may be a natural hybrid with sour orange (a sexual hybrid of pummelo and mandarin) as the seed parent and mandarin as the pollen parent. The cultivated landrace 'Huarongdao Zhoupigan' originated in China, and it has a history of more than a hundred years. It is widely cultivated for its distinctive pericarp, soft juicy pulp, slight bitter taste, and rich flavonoids and vitamin C (17.2 ± 0.08 mg•mL−1). Morphological observation shows that 'Huarongdao Zhoupigan' is mandarin-like in leaf shape, fruit flesh, easy peeling and crumpled pericarp, implying this variety may be a hybrid of orange and mandarin. To reveal the genetic background of 'Huarongdao Zhoupigan', 21 citrus accessions were evaluated using nuclear and chloroplast SSR markers and whole-genome SNP information. 'Huarongdao Zhoupigan' was grouped with mandarins and closely clustered with 'Yuanjiang Nanju' in the nuclear SSR analysis and sub-grouped with 'Goutou' sour orange, 'Dahong' sweet orange and 'Newhall' navel orange in the chloroplast SSR analysis. The genomic sequence similarity rate of 'Huarongdao Zhoupigan' with mandarin was 36.09%, with mandarin heterozygosity of 46.50%; the rough ratio of the two main parts was nearly 1:1, except for the unknown (19.11%) and pummelo (1.46%) parts. Thus, 'Huarongdao Zhoupigan' may be a natural hybrid with sour orange (a sexual hybrid of pummelo and mandarin) as the seed parent and mandarin as the pollen parent. [ABSTRACT FROM AUTHOR]