Some species of oysters are ecosystem engineers that form biogenic reef structures (oyster reefs) in shallow coastal and estuarine systems around the world. Unsustainable and destructive harvesting coupled with pollution, disease, and coastal development has resulted in declines of approximately 85 % of the worlds oyster reefs, making them one of the most threatened marine ecosystems on the planet. They are now considered to be functionally extinct or critically endangered in most parts of North America, Europe and Australia which has triggered a restoration movement to re-establish lost ecosystem services. Oyster reefs were previously thought to be temperate and subtropical ecosystems, but we now know that they also occur throughout the global tropics. Tropical oyster reefs have often been excluded from global assessments of historical distributions, declines and conservation needs. As a result, there are major knowledge gaps for tropical oyster reefs, including about which species are reef-building, structural characterisations of remnant reefs, and associated biodiversity. To address these knowledge gaps, I conducted a literature review (Chapter 2) to compare the diversity of reef-building oyster species between temperate and tropical regions, assess tropical oyster reef declines, and summarise the known biology, ecology, and benefits of tropical oyster reefs. I found that the diversity of reef-building oysters is four times higher in tropical than temperate regions, and that there is strong evidence of oyster reef declines. The high diversity, morphological plasticity, shared characteristics and overlapping distributions of tropical oysters has resulted in misidentifications and taxonomic ambiguities. Genetic barcoding has proven essential for accurate species identification and understanding species geographic ranges, however, associated costs can be high, and barcoding success rates are notoriously low in bivalves. To enable easy and cost-effective identification of five Saccostrea species commonly found in Queensland, Australia, I developed a series of species-specific primers that can be used in multiplex assays for species identification (Chapter 3). The practical application of these primers was verified on wild spat collected from Moreton Bay, and by their successful incorporation into a non-destructive protocol for species identification from pallial fluid. There is growing interest in oyster reef restoration in Queensland, however, efforts are currently focused on the Sydney rock oyster Saccostrea glomerata. Tropical oysters commonly form mixed species reefs and there are multiple species of Saccostrea in Queensland (Chapter 2). Settlement patterns among co-occurring species are poorly understood, largely due to the challenges of morphological identification and the lack of understanding of local reef-building Saccostrea species. Using the multiplex assays for Saccostrea spp identification, I collected and identified oysters in the Noosa estuary to better understand settlement patterns between co-occurring oysters, and to assess reef-building capabilities of additional Saccostrea species (Chapter 4). S. glomerata was found to be the most common species and adults occurred in both the upper and lower intertidal zone, however, Saccostrea lineage G was found almost exclusively in the lower intertidal zone, indicating that this species occupies a distinct tidal niche. Due to the low numbers detected it is unclear whether lineage G can be defined as reef-building, however targeting this species in restoration projects may increase the total vertical height of reefs and add structural complexity in the lower intertidal zone. Finally, I compared the characteristics of three newly documented oyster reefs in Queensland to gain a foundational understanding of their ecology. Reef-building oysters identified using multiplex assays from Chapter 3 were predominantly Saccostrea lineage B, a species distributed across tropical Australia and the Indo-Pacific. At each location, structural reef traits were assessed, and associated invertebrate communities quantified taxonomically and functionally. Location had a strong effect on invertebrate communities, with reefs in Gladstone hosting a greater abundance, and larger, invertebrates, followed by Mapoon, and then Proserpine. Most invertebrates were positively associated with the lower intertidal zone and shelly sediment, and we suggest that heat stress, interstitial reef spaces, and the proportion of habitat edges were likely explanations for these observed patterns. By assigning functional groups and accounting for invertebrate size, we show how the service provision of reef-associated invertebrates can be incorporated into reef characterisations and assessments of overall reef function. These characterisations provide insights into the ecology of tropical oyster reefs for conservation and provide baseline information to inform appropriate restoration strategies and monitoring metrics.