BackgroundJoint efforts by government and non-government organizations have helped to reduce malaria in Bangladesh and set the country on a clear path to eventual malaria elimination. However, achieving that goal would be challenging without a comprehensive understanding of vector bionomics.MethodsTargeted capturing ofAnophelesmosquitoes over a rainy season, utilizing specific sampling methods, including human landing catches (HLCs), CDC-light traps (CDC-LTs), and pyrethrum spray catches (PSCs) were aimed to characterize entomological drivers of transmission in four sites of Bandarban, Bangladesh.ResultsMolecular characterization of a subset of 4637 mosquitoes has demonstrated the presence of at least 17 species whose capture rates were representative of the rainy season. Species compositions and bionomic traits did not vary between sites withAnopheles maculatushaving the highest landing rate by HLCs andAnopheles vagushaving the highest capture rate with CDC-LTs. Interestingly,Anophelesspecies compositions and capture rates varied significantly (p < 0.05) forAn. vagus, between HLCs and its often-used proxy—CDC-LTs- suggesting impacts on downstream analysis. CDC-LTs capture rates demonstrated differing compositions with indoor and outdoor biting rates. For example,Anopheles nigerrimusandAnopheles nivipeswere more endophagic by HLCs and more exophagic by CDC-LTs. The use of a cow-baited CDC-LT also demonstrated significantly different results when compared to a human-baited CDC-LT considering the high degree of anthropophily in these species. The exception to both zoophily and indoor resting wasAn. vagus, which demonstrated both anthropophily and high resting rates indoors—pointing to this species being a possible primary vector at this site.ConclusionA diverseAnophelesfauna in Bandarban has been confirmed through molecular methods, highlighting the potential impact of sampling techniques. Given the complexity of the local ecosystem, a better understanding of mosquito behaviour and ecology is required to achieve the goal of malaria elimination in Bangladesh.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12936-023-04614-2.