Megaselia scalaris (Diptera: Phoridae), humpbacked, coffin or scuttle fly, is considered as a cosmopolitan scavenging insect. Despite its profound value in Forensic Entomology and biological control, M. scalaris is regarded as a medically notable insect worldwide because it is source of myiasis diseases. Further, it was recorded as a parasitoid infesting some useful insects. On the other hand, it attacks some plants such as corn, food and seed deposits, germinated seeds, cultivated and non-cultivated mushroom and fruits like bananas. Feeding on such infected fruits, can cause intestinal and wound myiasis. Therefore, scuttle fly should be controlled for human welfare and economic reasons. Phytochemical insecticides may be effective, safe and acceptable alternative to traditional chemical insecticides. Thymol, a constituent of oil of thyme (Thymus vulgaris), is widely used as food flavorings, mouthwashes, pharmaceutical preparations, besides it has many pesticidal uses; as insecticide, fungicides, rodenticide and antimicrobial effect. Moreover, it degrades rapidly and has no negative effect on seed germination. Accordingly, the present study was conducted to investigate the effects of thymol on the mortality, morphology and surface ultrastructure of the 3rd instar larvae of M. scalaris. Results showed that thymol has larvicidal effect, as the estimated LC50 averaging 5.22 g/100g media, and the response was a dose-dependent. Morphological observations revealed that thymol treatment resulted in different morphogenic malformations in larval stage. Malformed larvae appeared sluggish and motionless, with symptoms of distorted, darkened and dry bodies. On the other hand, at the ultrastructural level, thymol treatment exhibited many morphological aberrations as compared with the controls. Such aberrations appeared in the malformed structure of short spinous processes and spines of the body wall, bubble membranes, antennae, mouth hooks, maxillary palp complexes and anterior and posterior spiracles. Based on the present results, it is concluded that thymol can prevent adult emergence through killing maggots and protect against re-infestation. Consequently, thymol could be suggested as a safe effective larvicide against the scuttle fly larvae.