Coral disease represents one of the many challenges facing coral reefs, and is a contributing factor to the overall decline in coral reef health worldwide. An increase in disease frequency, outbreaks and the emergence of new diseases has fuelled much concern over the impact of coral diseases and subsequently prompted research into their possible causes. Our understanding of putative coral pathogens has lagged behind the emergence of coral disease as a major threat to the health of coral reefs. The Great Barrier Reef (GBR) is the largest contiguous reef in the world, and is still regarded as one the healthiest and best managed coral reef ecosystems in existence today. Despite this, the frequency of coral disease has begun to increase sharply over the past decade, prompting researchers to focus on the aetiology, causal factors and ecological impact of coral disease within the Great Barrier Reef Marine Park (GBRMP). This PhD thesis focused on two distinct disease elements: brown band (BrB) and white syndrome (WS). These two diseases affect corals within the GBRMP, yet their microbiology and ecology is largely unknown. The research project investigated the microbiology and ecology of WS and BrB affecting acroporids, using culture-dependent and independent methods to characterise the microbial community associated with healthy and diseased corals and identify putative coral pathogens. The lifecycle and diurnal cycles of BrB ciliates were also explored to gain a greater understanding of the effect of these ciliates on coral health. Ecological surveys were carried out at Heron Island sites commonly used for the collection of corals to ascertain the prevalence and significance of these diseases in the context of laboratory results. Surveys at five sites revealed a mean prevalence of 8.11% of tabular acroporids affected by WS, which is consistent with previous studies. BrB revealed a much lower prevalence of less than 0.04%. Bacterial 16S rRNA gene clone libraries were constructed from Acropora hyacinthus samples derived from a healthy control colony, and a healthy section and lesion border of a WS affected colony. Distinct shifts in the microbial community and partitioning between the lesion border and healthy section of the diseased colony were observed. In addition, the healthy section of the diseased colony displayed a different microbial community to the control colony, supporting previous data that a microbial shift occurs preceding visible signs of infection. A number of bacteria from the healthy section of diseased coral shared close sequence affiliations to a number of Vibrio spp., including potentially pathogenic Vibrio species. Sequences retrieved from the lesion border of WS affected Acropora hyacinthus were dominated by Pseudoalteromonas spp., although these species have not been previously implicated in coral disease. The coral disease BrB is characterised by the presence of a brown ciliate band and these ciliates have been identified as a new species belonging to the class Oligohymenophorea, subclass Scuticociliatia. Within BrB-affected Acropora muricata, numerous filamentous, coccoid and rod bacteria were observed to be closely associated with the ciliate band, but absent in coral tissue adjacent to the typical brown band. It is unknown whether the bacteria associated with the mass of ciliates are the primary pathogens, a food source for the ciliates or simply opportunistic pathogens. Several isolates retrieved from BrB corals were tested for their pathogenicity in controlled infection trials using Acropora muricata. The preliminary results identified at least two isolates of interest (CC1 and HB-8). However, the results of a replicated infection trial failed to conclusively identify the bacteria as the causative agents of this disease. The findings from the cross-infection trials and ecological surveys suggest that BrB is an infectious but not highly contagious coral disease. This study revealed important aspects of both WS and BrB that were previously unknown. The research carried out has built a greater understanding, and a platform for future research directed at understanding key processes involved in these coral diseases. This research has highlighted the need for ongoing infection trials in diseases, even when a pathogen has been identified. The discovery of possible key bacterial species involved in WS and BrB warrants further research aimed at understanding the mechanisms in which bacteria may affect the coral holobiont. In conclusion, this research has further supported the notion that corals are a complex community with bacterial, animal and protistan partners, which when disturbed may see one or several of the previous benign partners becoming pathogenic. In a rapidly changing climate, this conclusion is consistent with the idea that coral diseases are on the rise due to changing environmental circumstances disturbing the balance between these interdependent partners.