The koala (Phascolarctos cinereus) is an arboreal herbivorous marsupial that is an Australian icon. It is widely accepted that koala populations are declining at an increased rate with recent studies suggesting that the strongest contributing factor to this population decline is the prevalence of disease. Chlamydia pecorum and Chlamydia pneumoniae are obligate intracellular Gram-negative bacteria that cause abortion, infertility, arthritis, conjunctivitis, respiratory disease, and in some cases death in koala populations. Due to a lack of koala-specific immune reagents and assays there is no way to adequately analyse the immune response in diseased, healthy or vaccinated animals. Using sequence homology and available transcriptome data cluster of differentiation markers expressed by key lymphocyte subsets and key soluble koala immune molecules were identified and expressed as recombinant proteins to produce monoclonal antibodies. Following the collection of primary koala spleen and lymph node cells the verification of each antibody was performed through Western Blot, ELISA, Immunohistochemistry, qPCR and Flow Cytometry analysis. The koala specific monoclonal antibodies were then used to investigate the cellular response to infection/vaccination of chlamydia through flow cytometry and ELISA assays. This research project will provide the first in depth understanding of the koala immune system in response to chlamydial infection by developing a suite of species specific immune reagents and characterising immune profiles of healthy, diseased and vaccinated animals. The reagents and techniques developed from this project are applicable to further understand the koala immune response to other diseases and injury.