Parasitism is a significant cause of stranding and mortality in endangered sea turtles. Two parasites in particular (or groups thereof) have been noted for their impacts on green sea turtle populations. The first are the spirorchiid blood flukes, which inhabit the circulatory systems of their host. The second is the eimeriid coccidian Caryospora cheloniae, a systemic parasite affecting a number of organs. Diversity among these organisms is poorly explored, and is almost certainly greater than currently recognised. The parasites and their associated diseases fluctuate both temporally and spatially in terms of prevalence and severity, however, the factors driving these fluctuations are poorly understood. A variety of questions remain unanswered in terms of the epidemiology and relative pathogenicity of the different parasite species. Of particular interest are brain lesions, which have been associated with both parasites and in some cases lead to neurological deficiency and subsequent mortality. Difficulties in finding answers to these questions is compounded by a lack of reliable, fast and quantitative ante-and post-mortem diagnostic tools for either parasite, which restricts their investigation.In order to catalogue local species and assess diversity, adult spirorchiid flukes were collected during post-mortem examination of deceased sea turtles and characterised by molecular and morphological means. Eleven distinct species or genotypes were identified, comprising a mix of previously described and novel species or variants. Samples were also collected from green sea turtles that died during a coccidiosis related mass mortality event in south east Queensland and northern New South Wales. While only one species of coccidian (C. cheloniae) had been previously described, molecular characterisation of the organism implicated in the outbreak revealed two distinct coccidian genotypes, which has significant implications for diagnosis and management.Spirorchiid ova have been associated with granulomatous lesions in a wide range of host tissues. However, it has not been possible to identify spirorchiids beyond the genus level based on morphology, which has frustrated any attempts to identify the species or variants responsible for severe lesions. In this thesis, a molecular approach was used and a terminal restriction fragment length polymorphism (T-RFLP) assay was developed to detect and identify individual species within the often mixed assemblages of ova in turtle tissues. This assay proved to be a more specific and sensitive alternative to traditional iii microscopic detection methods. Through correlation with histopathology and gross pathology, the tissue tropisms, relative occurrence and pathogenicity of each species were investigated. The most common species (Neospirorchis Genotype 2) was found in 96% of samples, encompassing tissues from all organs sampled. On average, a greater number of spirorchiid species were detected in tissues where lesions were present, and numbers increased along with the severity o...