The larva of stone leek leafminer, Liriomyza chinensis (Kato), is known to infest alternately just below the epidermis and inner surface of hollow cylindrical leaves of allium crops, resulting in the formation of discontinuous linear mines (mine form: discontinuous). However, after the fall of 2016, a novel mine form of the same species (mine form: continuous) was detected in Welsh onion fields of Kyoto Prefecture, Japan. We hypothesized that these mine forms were associated with flies having different genetic backgrounds; hence, we compared the mine forms and the partial mtCOI gene of flies collected from Welsh onion fields from 2018 to 2019. The results demonstrated that the flies that emerged from different mine forms could be classified into two haplogroups, i.e., flies displaying a discontinuous mine form were of haplogroup A, whereas those that displayed continuous mines were of haplotype B. Additionally, using populations of these flies reared in the laboratory, we confirmed that the mine form of the larvae of haplotype A on Welsh onions was discontinuous, whereas that of haplotype B was continuous. We named the population that exhibited a discontinuous mine form as biotype A and the population displaying a continuous mine form as biotype B.