Production and productivity of hot pepper is highly threatened by different diseases in Southern Ethiopia. However, the relative importance of each disease across locations has not been assessed and well profiled to sound management strategy. To determine the occurrence, distribution and the status of hot pepper diseases in the region, survey was carried out in seven districts i.e. Meskan, Mareko and Abeshge districts (in Gurage administrative zone), Dallocha and Lanfro (in Silte zone), Hawasa zuria (in Sidama zone) and Halaba special district in 2010 and 2011 cropping seasons. Results indicated that 55% of seed beds were infected by seedling diseases. The highest seedling infection (73%) was recorded at Hawassa zuria district followed by Halaba, Lanfro and Dalocha districts (60, 56 and 54%, respectively). Similarly survey results made after transplanting showed that 229 (75 %) of samples were infected at least by one disease. The frequency of pathogen growth depicted that 30% of the associated pathogens were different bacteria, while 21, 12, 9 and 3.0% belong to the fungal genera Fusarium, Colletotrichum, Cercospora and Alternaria spp respectively. Adoption analysis of previously recommended cultural practices showed 100%, 42%, 31%, 30% and 19% for fertilizer application, engagement in two year rotation, row planting, use of pesticides and improved seed, respectively. The current study indicated that a complex of diseases exist at each growth stage of hot pepper and the occurrence across districts is highly variable despite introduction and promotion of different management practices. Therefore holistic and cumulative integrated approach is required to manage the complex diseases in the region.