The aim of this article is to provide an overview of the current situation of coffee genetic resources that are dwindling at an alarming rate in Ethiopia, the centre of diversity of Coffea arabica. Firstly, we describe the coffee growing systems (forest coffee, semi-forest coffee, garden coffee and plantation coffee) and recent research on the genetic diversity of the coffee planting material associated with those systems. Whilst the maximum genetic diversity revealed by DNA-based markers is found in the forest coffees of the south-western highlands, the natural habitat of C. arabica, the taxonomy of coffee landraces is particularly rich in garden coffee systems located in ancient growing zones such as Harerge in eastern Ethiopia. After reviewing the factors involved in the genetic erosion of the Ethiopian genepool, we give an update on the status of coffee genetic resources conserved ex situ in the field genebank of the Jimma Agricultural Research Centre, with 4,780 accessions spread over 10 research stations located in the main production areas, and in the main genebank of the Institute of Biodiversity Conservation located in Choche (Limu) with 5,196 accessions conserved. Lastly, we mention the in situ conservation operations currently being implemented in Ethiopia. Improving our knowledge of the genetic structure of Ethiopian forest and garden coffee tree populations as well as genetic resources conserved ex situ will help to plan the future conservation strategy for that country. To this end, modern tools as DNA-based markers should be used to increase our understanding of coffee genetic diversity and it is proposed, with the support of the international scientific community and donor organizations, to undertake a concerted effort to rescue highly threatened Arabica coffee genetic resources in Ethiopia.