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Meliponiculture, the keeping of domesticated stingless bees such as <i>Geniotrigona thoracica</i> (Smith, 1857) (Hymenoptera: Apidae), is an increasingly popular agricultural industry in Malaysia. This study reports the soldier fly (Diptera: Stratiomyidae) species of the genus <i>Hermetia</i> colonizing stingless bee colonies in Malaysia. The larvae were reared in the laboratory to the adult stage and identified through molecular and morphological approaches. <i>Hermetia illucens</i> (Linnaeus, 1758) and <i>Hermetia fenestrata</i> de Meijere, 1904 (Diptera: Stratiomyidae) were identified from the sample provided. Earlier records of stratiomyids in stingless bee nests were misidentified as <i>H. illucens</i>. This paper represents the first identified record of <i>H. fenestrata</i> 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.