Marine turtle numbers are in a state of flux around the world. Six of the seven remaining species of these long-lived animals are threatened; with the seventh being listed data deficient. Reasons for these fluctuations are speculated to be due to human related impacts (direct) and increase in disease occurrence caused by changes in the natural environment (indirect). Most direct impacts have been identified and strategies implemented to mitigate their effects with varying degrees of success; however the indirect effects on marine animals remain an understudied area. This thesis outlined the development of ante- and post-mortem diagnostic techniques to identify prevalent diseases affecting two marine turtle species in southern Queensland over a four year (2006-2009) period. This data was used to determine the impact of disease on turtle survivorship. Two-hundred and ninety green turtles (Chelonia mydas) from Moreton and Shoalwater Bays were captured, clinically assessed and blood sampled. Clinically healthy animals (n = 211) were used to derive biochemical and haematological reference intervals using two methods. Comparisons with clinically unhealthy animals (n = 25) indicated all unhealthy animals had at least some plasma biochemical and haematological values outside the derived intervals (albumin, 48% of unhealthy animals; alkaline phosphatase (ALP), 35%; aspartate transaminase (AST), 13%; creatinine, 30%; globulin, 3%; glucose, 34%; lactic dehydrogenase (LDH), 26%; phosphorus, 22%; sodium, 13%; thrombocytes, 57%; and monocytes, 5%). Amongst small immature animals, those with Chelonibia testudinaria plastron barnacle counts of at least 20 were approximately three times more likely to be unhealthy than turtles with no barnacles. In addition, small immature and mature turtles were more likely to be unhealthy than large immature turtles (Chapter 2). By the same method, 101 loggerhead turtles (Caretta caretta) in Moreton Bay were assessed and bled. Clinically healthy animals (n = 63) were used to derive intervals. Comparisons with clinically unhealthy animals (n = 23) indicated 82% and 45% had at least one biochemical and hematological result, respectively, outside of at least one of the calculated intervals. Neither sex nor maturity (mature versus large immature) influenced the risk of being clinically unhealthy (Chapter 3). A standardised approach to post-mortem examination of marine turtles for veterinary clinicians with a concurrent descriptive review of gross and microscopic pathological lesions commonly seen during examination in Australia (Chapter 4) was used to accurately determine diseases and causes of death in 100 green turtles submitted from various regions of southern Queensland for examination. Spirorchiid parasitism was found to be the most frequently occurring cause of mortality (41.8%), followed by gastrointestinal impaction (11.8%), microbiological infectious diseases (5.2%) and trauma (5.2%). Spirorchiid parasitism with associated inflammation (75%) was the most frequently occurring disease followed by gastrointestinal impaction (5.1%). Season and turtle age had limited influences on disease. Severity of spirorchiidiasis in the brain was independent of severity in other organs (Chapter 5). From these examinations, the most prevalent disease syndrome (spirorchiidiasis) and a previously unreported finding in Australian waters (corneal fibropapillomatosis) were selected to be examined in greater detail. Spirorchiid parasites from four organs in five green turtles were identified by established morphological and molecular techniques. Morphological study of adults identified Carettacola sp. in the serosal wall of the gastrointestinal tract, Hapalotrema mehrai in the heart and Learedius learedi in the spleen. Worms from the brain probably belonged to the genus Neospirorchis. DNA sequences from a portion of the 28S ribosomal RNA gene were obtained; but only matches for Hapalotrema mehrai and Learedius learedi were made. The prevalence and severity of this disease warrants further investigation into development of molecular techniques for use as a prognostic tool for turtles entering rehabilitation (Chapter 6). Chelonid corneal fibropapillomatosis, a previously unreported disease manifestation in Australia, was identified in 0.5% of 787 examined green turtles in 2008 (Chapter 7). This novel syndrome was shown to reduce visibility, potentially negatively affecting turtle survivorship and should be monitored for further spread. Findings from this thesis and the published literature were used to derive a mathematical model to determine the effects of identified diseases on Moreton Bay green turtle survivorship. This model demonstrated diseases at current prevalence will not negatively affect survivorship but an adverse environmental disruption or an increase in current disease frequency may threaten these animals (Chapter 8). Information presented in this thesis was used to test the general hypothesis ‘Differences in disease and health between stranded and functional populations of marine turtles will indicate major and currently unmeasured causes of population decline.’ This hypothesis was partially upheld. Differences in disease and health status between stranded and functional populations were demonstrated, but more work is required to comprehensively examine these statuses. Diagnostics and continued environmental assessment should become the focus of future investigations. These findings should be incorporated in future management strategies.