Most Korean beekeepers have moved from south to north of Korea to collect nectar from black locust (Robinia pseudoacacia) flowers for 2 months. This provided a valuable opportunity to sample bees originating from diverse areas in one location. We initiated a survey of honeybee (Apis mellifera) colonies on the blooming period of Acacia to determine the prevalence of Nosema apis and black queen cell virus (BQCV) in 2013. Nosema causes significant losses in population size of honeybees. Sixteenth hives were sampled for this study. Bees were collected on the 4th and 13th of May, 2013. Nosema spore counts ranged from zero to 1,948,333 spores per bee. The average number of nosema spores per bee was calculated to be 450,000. Approximately 94% of the apiaries examined were infected with nosema, based on the presence of spores in the flowering period of Acacia. Also nosema is thought to be associated with black queen cell virus. RT-PCR analysis shows that BQCV infection rate was 100%. This indicates that nosema and BQCV is the predominant species affecting honeybee colonies.