Djiboutian coral reefs are poorly studied, but are of critical importance to tourism and artisanal fishing in this small developing nation. In 2014 and 2016 we carried out the most comprehensive survey of Djiboutian reefs to date, and present data on their ecology, health and estimate their vulnerability to future coral bleaching and anthropogenic impacts. Reef type varied from complex reef formations exposed to wind and waves along the Gulf of Aden, to narrow fringing reefs adjacent to the deep sheltered waters of the Gulf of Tadjoura. Evidence suggests that in the past 35 years the reefs have not previously experienced severe coral bleaching or significant human impacts, with many reefs having healthy and diverse coral and fish populations. Mean coral cover was high (52%) and fish assemblages were dominated by fishery target species and herbivores. However, rising sea surface temperatures (SSTs) and rapid recent coastal development activities in Djibouti are likely future threats to these relatively untouched reefs.