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Background  Defence mechanisms of organisms are shaped by their lifestyle, environment and pathogen pressure. Carpenter ants are social insects which live in huge colonies comprising genetically closely related individuals in high densities within nests. This lifestyle potentially facilitates the rapid spread of pathogens between individuals. In concert with their innate immune system, social insects may apply external immune defences to manipulate the microbial community among individuals and within nests. Additionally, carpenter ants carry a mutualistic intracellular and obligate endosymbiotic bacterium, possibly maintained and regulated by the innate immune system. Thus, different selective forces could shape internal immune defences of  Camponotus floridanus .    Results  The immune gene repertoire of  C. floridanus  was investigated by re-evaluating its genome sequence combined with a full transcriptome analysis of immune challenged and control animals using Illumina sequencing. The genome was re-annotated by mapping transcriptome reads and masking repeats. A total of 978 protein sequences were characterised further by annotating functional domains, leading to a change in their original annotation regarding function and domain composition in about 8 % of all proteins. Based on homology analysis with key components of major immune pathways of insects, the  C. floridanus  immune-related genes were compared to those of  Drosophila melanogaster ,  Apis mellifera , and other hymenoptera. This analysis revealed that overall the immune system of carpenter ants comprises many components found in these insects. In addition, several  C. floridanus  specific genes of yet unknown functions but which are strongly induced after immune challenge were discovered. In contrast to solitary insects like  Drosophila  or the hymenopteran  Nasonia vitripennis , the number of genes encoding pattern recognition receptors specific for bacterial peptidoglycan (PGN) and a variety of known antimicrobial peptide (AMP) genes is lower in  C. floridanus . The comparative analysis of gene expression post immune-challenge in different developmental stages of  C. floridanus  suggests a stronger induction of immune gene expression in larvae in comparison to adults.    Conclusions  The comparison of the immune system of  C. floridanus  with that of other insects revealed the presence of a broad immune repertoire. However, the relatively low number of PGN recognition proteins and AMPs, the identification of  Camponotus  specific putative immune genes, and stage specific differences in immune gene regulation reflects  Camponotus  specific evolution including adaptations to its lifestyle.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1748-1) contains supplementary material, which is available to authorized users.

Scrutinizing the immune defence inventory of Camponotus floridanus applying total transcriptome sequencing