The purpose of this study was to determine the prevalence of trachoma in evaluation units (EUs) of grouped districts (woredas) in Southern Nations, Nationalities, and Peoples’ Region (SNNPR), Ethiopia. A population-based prevalence survey was conducted in 2013-2014 in each EU according to the methodology of the Global Trachoma Mapping Project. The study concluded that active trachoma and trichiasis are significant public health problems in SNNPR and full implementation of the SAFE strategy (Surgery, Antibiotics, Facial cleanliness, and Environmental improvement) is required. Specifically 38 of the 40 EUs surveyed require Mass Drug Administration (MDA) with azithromycin for at least 3 years, plus implementation of the F and E components of the SAFE strategy, before impact surveys. The prevalence of trichiasis was above the WHO elimination threshold of 0.2% in 37 EUs.