Abstract Background Midgut invasion, a major bottleneck for malaria parasites transmission is considered as a potential target for vector-parasite interaction studies. New intervention strategies are required to explore the midgut proteins and their potential role in refractoriness for malaria control in Anopheles mosquitoes. To better understand the midgut functional proteins of An. culicifacies susceptible and refractory species, proteomic approaches coupled with bioinformatics analysis is an effective means in order to understand the mechanism of refractoriness. In the present study, an integrated in solution- in gel trypsin digestion approach, along with Isobaric tag for relative and absolute quantitation (iTRAQ)–Liquid chromatography/Mass spectrometry (LC/MS/MS) and data mining were performed to identify the proteomic profile and differentially expressed proteins in Anopheles culicifacies susceptible species A and refractory species B. Results Shot gun proteomics approaches led to the identification of 80 proteins in An. culicifacies susceptible species A and 92 in refractory species B and catalogue was prepared. iTRAQ based proteomic analysis identified 48 differentially expressed proteins from total 130 proteins. Of these, 41 were downregulated and 7 were upregulated in refractory species B in comparison to susceptible species A. We report that the altered midgut proteins identified in naturally refractory mosquitoes are involved in oxidative phosphorylation, antioxidant and proteolysis process that may suggest their role in parasite growth inhibition. Furthermore, real time polymerase chain reaction (PCR) analysis of few proteins indicated higher expression of iTRAQ upregulated protein in refractory species than susceptible species. Conclusion This study elucidates the first proteome of the midguts of An. culicifacies sibling species that attempts to analyze unique proteogenomic interactions to provide insights for better understanding of the mechanism of refractoriness. Functional implications of these upregulated proteins in refractory species may reflect the phenotypic characteristics of the mosquitoes and will improve our understandings of blood meal digestion process, parasite vector interactions and proteomes of other vectors of human diseases for development of novel vector control strategies. Electronic supplementary material The online version of this article (10.1186/s12864-018-4729-3) contains supplementary material, which is available to authorized users. Keywords: Anopheles culicifacies, Refractory, Midgut, Shot gun proteomics, iTRAQ, RT-PCR Background According to World Health Organization (WHO), India accounts for 75% of total malaria cases among South East Asia region [[35]1]. Female mosquitoes of the genus Anopheles are the major protagonists of malaria transmission. Among various Anopheles species, Anopheles culicifacies is considered as one of major malaria vector responsible for transmitting nearly 65% of total malaria cases in India [[36]2]. This rural malaria vector species has been characterized as a sibling species complex with five sub species designated as A, B, C, D and E. All these sibling species are phylogenetically indistinguishable and are discriminated on the basis of vectorial capacity and malaria transmission rate [[37]3]. A natural sub species of An. culicifacies, species B was detected and isolated from a specific area that is found to be refractory (poor vector) against human malaria parasites Plasmodium vivax (100% refractory) and Plasmodium falciparum (partially) [[38]4]. Both potent and poor vector species however, display same distribution and adaptation to environment with similar zoophilic feeding preferences for human and cattle [[39]5].