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Background  Clarifying the role of the innate immune system of the malaria vector  Anopheles gambiae  is a potential way to block the development of the  Plasmodium  parasites. Pathogen recognition is the first step of innate immune response, where pattern recognition proteins like GNBPs play a central role.    Results  We analysed 70 sequences of the protein coding gene  GNBPB2  from two species,  Anopheles gambiae  ( s.s. ) and  An. coluzzii , collected in six African countries. We detected 135 segregating sites defining 63 distinct haplotypes and 30 proteins. Mean nucleotide diversity (π) was 0.014 for both species. We found no significant genetic differentiation between species, but a significant positive correlation between genetic differentiation and geographical distance among populations.    Conclusions  Species status seems to contribute less for the molecular differentiation in  GNBPB2  than geographical region in the African continent (West and East). Purifying selection was found to be the most common form of selection, as in many other immunity-related genes. Diversifying selection may be also operating in the  GNBPB2  gene.    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-016-1800-2) contains supplementary material, which is available to authorized users.

Molecular evolution and population genetics of a Gram-negative binding protein gene in the malaria vector Anopheles gambiae (sensu lato)