A cross-sectional study was conducted in Seka Chokersa district, Ethiopia from November, 2015 to June, 2016 with overall objective of assessing honeybee pests, parasites and pathogens; associated risk factors; and estimating their potential effects on beekeeping. A cluster of 3 beekeeping rural kebeles were randomly taken to select 245 sample beekeepers for questionnaire survey. A total of 60 honeybee colonies were randomly sampled. Semi-structured questionnaire was developed, and pretested for assessing of beekeepers' perception on honeybee pests, parasites, pathogens and associated predisposing conditions. Adult worker bees and bee brood were sampled from the sample honeybee colonies at each season. Samples were analyzed at Bee Protection Laboratory (BPL), Holeta Bee Research Center (HBRC), Ethiopia. Honeybee pests, namely Aethina tumida, Achrolla grisella, Ant spp, Gellaria mellonella, Spiders, Lizards, Bee Eating Birds, Mice and Honey badgers were known to exist in the study area.Comparatively, Aethina tumida, Achrolla grisella and Varroa Destructor were identified the most abundant honeybee pests. Apparent reduction in honeybee population and honey production was observed in the pest affected honeybee colonies. It is suggested that detailed and large scale study be conducted to declare the actual absence of those honeybee pests, parasites and pathogens (which were not tested positive) to help complete these study to the best of its anticipated purpose. It is worth noting that the current research has documented present status for major honeybee pests and parasites in the study area and, therefore can bestow basic information for all stake-takers in designing any of their research and development endeavors with regard to the subsector.