Background: Clogmia albipunctata is cosmopolitan in distribution. The adult flies can survive and spread outdoors during the temperate seasons while continuously breeding in buildings during the winter months. Because they are non-biting, tiny and quite, most of people do not pay special attention to them. It is the first case reported that Clogmia albipunctata larvae cause human residual root myiasis.Case presentation: In December 2020, a 26-year-old woman was referred from Kaifeng New District Maternal and Child Health Care Hospital to the Department of Pathogenic Biology, Medical College of Henan University with chief complaint that two active alive larvae were found in the mouth while brushing her teeth in the morning. The intraoral examination revealed nice oral hygiene and no larvae was found directly. The right second mandibular molar was a residual root and the mucosa above it was mild erythematous and edematous and no bleeding on probing was present. While some 50℃ normal saline was injected in the residual root with syringe, four larvae swarmed out from the residual root. The larvae were observed by naked eyes and light microscope and the larvae were reared. One adult fly was got 11 days later. They were identified as Clogmia albipunctata larvae. Because the patient was in lactation, medication was not recommended. Treatment included the removal of all visible larvae followed by debridement. The patient was followed-up for 1 month and healed. The patient’s residual root myiasis was associated with sleeping with the mouth open and the smell of rotten food in the residual root attracted Clogmia albipunctatus to lay eggs in the residual root.Conclusions: This report implies that even if the oral hygiene is nice in general, the existence of residual roots maybe results in oral myiasis. The myiasis caused by Clogmia albipunctata larvae should be paid attention to. It is necessary to treat residual roots in time.