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Background  The midgut microbiota of mosquitoes maintain basal immune activity and immune priming. In recent years, scientists have focused on the use of microbial communities for vector control interventions. In the present study, the midgut bacteria of larvae and adults of  Aedes aegypti  and  Ae. albopictus  were assessed using both field-collected and laboratory-reared mosquitoes from Sri Lanka.    Methods  Adults and larvae of  Ae. aegypti  and  Ae. albopictus  were collected from three selected areas in Gampaha Medical Officer of Health area, Gampaha District, Western Province, Sri Lanka. Bacterial colonies isolated from mosquito midgut dissections were identified by PCR amplification and sequencing of partial  16S rRNA  gene fragments.    Results  Adults and larvae of  Ae. aegypti  and  Ae. albopictus  harbored 25 bacterial species.  Bacillus endophyticus  and  Pantoea dispersa  were found more frequently in field-collected  Ae. aegypti  and  Ae. albopictus  adults, respectively. The midgut bacteria of  Ae. aegypti  and  Ae. albopictus  adults ( X  2  = 556.167,  df  = 72,  P  < 0.001) and larvae ( X  2  = 633.11,  df  = 66,  P  < 0.001) were significantly different. There was a significant difference among the bacterial communities between field-collected adults ( X  2  = 48.974,  df  = 10,  P  < 0.001) and larvae ( X  2  = 84.981,  df  = 10,  P  < 0.001).  Lysinibacillus sphaericus  was a common species in adults and larvae of laboratory-reared  Ae. aegypti.  Only  P. dispersa  occurred in the field-collected adults of  Ae. aegypti  and  Ae. albopictus . Species belonging to genera  Terribacillus ,  Lysinibacillus ,  Agromyces  and  Kocuria  were recorded from  Aedes  mosquitoes, in accordance with previously reported results.    Conclusions  This study generated a comprehensive database on the culturable bacterial community found in the midgut of field-collected ( Ae. aegypti  and  Ae. albopictus ) and laboratory-reared ( Ae. aegypti ) mosquito larvae and adults from Sri Lanka. Data confirm that the midgut bacterial diversity in the studied mosquitoes varies according to species, developmental stage and strain (field  vs  laboratory).    Graphical abstractSupplementary Information  The online version contains supplementary material available at 10.1186/s13071-021-04900-5.

Diversity of midgut bacteria in larvae and females of Aedes aegypti and Aedes albopictus from Gampaha District, Sri Lanka