Meliponiculture, the keeping of domesticated stingless bees such as Geniotrigona thoracica (Smith, 1857) (Hymenoptera: Apidae), is an increasingly popular agricultural industry in Malaysia. This study reports the soldier fly (Diptera: Stratiomyidae) species of the genus Hermetia colonizing stingless bee colonies in Malaysia. The larvae were reared in the laboratory to the adult stage and identified through molecular and morphological approaches. Hermetia illucens (Linnaeus, 1758) and Hermetia fenestrata de Meijere, 1904 (Diptera: Stratiomyidae) were identified from the sample provided. Earlier records of stratiomyids in stingless bee nests were misidentified as H. illucens. This paper represents the first identified record of H. fenestrata colonizing a “spoiled” stingless bee colony. In addition, adult and larval morphological differences between both species and the roles of both species in bee nest decomposition are discussed.