The synanthropic flies are regarded as the most important vectors of infectious diseases. Especially, feeding and reproductive habits make flies the important vectors of many pathogens such as malaria, yellow fever, dengue fever, typhoid fever, dysentery, and anthrax. Although most of lower flies (e.g. black-flies, mosquitos, sand-flies) transport diseases by bloodsucking, the mechanical dislodgment from exoskeleton is one of the important mechanisms of pathogens transmission for higher flies (Diptera: Brachycera) such as blow-flies, flesh-flies, and house-flies. According to recent phylogenetic studies, the Bibionomorpha is suggested as a sister taxon of the Brachycera as a monophyletic group “Neodiptera”. Coincidently, a part of black fungus gnats (Diptera: Bibionomorpha: Sciaridae) are known as the important vectors of fungal diseases on agricultural crops due to the spores carrying by there fore tibial structures. We propose that the correlation of spore carrying structures and habitats adaptation in the Sciaridae. The evolutionary pathway tests support that the fore tibia structures appeared first and followed by live plant habitats in the Sciaridae. Regarding analyses, we hypothesized that the evolutionary benefit of fungal carrying structures could be closely related with the larval habitats adaptation of Sciaridae. Interestingly, both adults of the synanthropic higher flies and the black fungus gnats are carrying various microorganisms by mechanical dislodgment from there tibial exoskeleton. The common habits of those flies could be providing clues about the evolution of the fly-microorganism interections.