Coffee diseases are presumed to be less important in the forest coffee as compared to the garden and plantation systems of coffee production in Ethiopia. In this article, the results of a study conducted on the occurrence and incidence of Coffee Wilt Disease (CWD) and the major factors influencing the disease in four major forests coffee sites in southwest and southeast Ethiopia are discussed. In each forest coffee site, coffee wilt syndrome was assessed in three systematically selected sample plots during dry and wet seasons of 2008 and 2009. Concurrently, three to four samples of infected coffee trees were randomly collected from each plot and the causal pathogen was isolated and identified in the laboratory. The result indicted that CWD was prevalent in the four forest coffee sites, with mean incidence of 27.1 and 29.2% in Harenna during 2008 and 2009 wet seasons, respectively, followed by Berhane-Kontir with mean incidences of 22.1 (2008) and 27.7% (2009). Whereas, Bonga and Yayu forest coffees had comparatively low wilt severity (<10%). The wood samples of most of the infected coffee trees (90.6%) yielded Gibberella xylarioides in the laboratory proving that this pathogen is the main cause of coffee tree death in the forest. The difference in incidence of CWD across the four sites and among fields was strongly associated with human factors and variations in coffee populations. The forest coffee trees in Harenna and Berhane-Kontir (high CWD) are almost transformed to semiforest type by sub-planting coffee seedlings after thinning the dense vegetation cover. These activities are known to create wound to the host and disseminate the fungus spores from tree to tree and from one field to the other. The two independent seedling inoculation tests in the greenhouse evidenced that there were significant variations among coffee accessions in reactions to CWD though most accessions were susceptible. The study showed that CWD is one of the potential biotic factors threatening the genetic diversity of Arabica coffee in most forest coffee sites and thus the disease management practices should duly be considered in planning and implementing forest coffee conservation strategy.