Recently, damage to Welsh onion, carrot, and Chinese chive by Bradysia odoriphaga Yang & Zhang, 1985 was reported from Saitama and Gunma Prefectures, Japan. Molecular identification methods are required to differentiate this species from other domestic sciarid flies. First, a PCR method using species-specific primers was developed to discriminate this species from three other sciarid species, Bradysia impatiens (Johannsen, 1912), Pnyxia scabiei (Hopkins, 1895), and Lycoriella ingenua (Dufour, 1839). Second, the applicability of a nondestructive DNA extraction method for this species was determined for cases where further morphological identification was required. It could be used for the morphological identification of specimens in addition to PCR using species-specific primers and DNA barcoding. Third, the lower limit of the proportion of this species in bulk samples of sciarid flies was determined. In larvae and male adults, one individual of this species could be detected in bulk samples (up to 800 individuals) of other species by PCR using species-specific primers. Further, it was revealed that specimens on the monitoring traps in the field should be collected within 8 days, regardless of the season. By combining these methods, an efficient identification method for monitoring this species was established using PCR with species-specific primers.