Genetic diversity of immune genes is critical for population-level resistance against infectious diseases. Studies in diversity of immune loci in wild species have almost exclusively focused on Major Histocompatibility Complex (MHC) genes; however these genes only account for a fraction of immune gene diversity. Tasmanian devils (Sarcophilus harrisii) are threatened with extinction by the spread of Devil Facial Tumour Disease. Devils are known to lack diversity at MHC and Toll-like receptor genes. Whether there are polymorphisms in devil immune genes more broadly is unknown. In this study, we characterised diverse immune gene families in the devil genome, and identified SNPs in a wide range of important immune genes. Using genome-level data from ten devils we identified SNPs within the exons, introns and flanking regions of 167 immune genes, including cytokines, chemokines and natural-killer cell receptors. From this data, we developed long-amplicon assays to target nine key genes which were sequenced in up to 220 devils. We found an extreme paucity of genetic diversity across a broad range of immune genes. Despite this, signatures of balancing selection were exhibited by one chemokine gene, suggesting that remaining diversity may hold adaptive potential. The low functional diversity may leave devils highly vulnerable to infectious disease; therefore monitoring and preserving remaining diversity is critical for the long-term management of this species. Examining genetic variation in diverse immune genes should be a priority for threatened wildlife species. This study can act as a model for broad-scale immunogenetic diversity analysis in wild populations.