A cross-sectional survey was carried out between July and October 2015 across three apiaries in the Ijebu North Local Government Area of Ogun State, southwestern Nigeria to assess the parasites associated with the honeybee (Apis mellifera). Two-hundred honeybees were collected twice a month from the colonies in each of the apiaries to detect and identify ectoparasites using the ethanol wash method. Fifty honeybees (one quarter) were sampled from the selected colonies in each of the apiaries and subjected to microscopic examination and dissection for the assessment of associated endoparasites. All the colonies sampled were infested with Varroa destructor and the developmental stages of Acarapis woodi, although there was no significant difference (P > 0.05) observed in the infestation levels of all the colonies sampled. The mean of V. destructor infestation (12.70 ± 1.73/bee/colony) was recorded to be significantly higher in the bee colonies from Imosan apiary in July compared to those sampled from Ogbe (8.70 ± 1.51/bee/colony) and O.O.U. Ago-iwoye (6.10 ± 0.86/bee/ colony) apiaries. There was no significant difference (P > 0.05) in the mean numbers of bees per colony with light A. woodi infestation recorded in July, August, September and October across apiaries in Ogbe (42.35 ± 1.0/bee/colony), Imosan (40.23 ± 1.0/bee/ colony) and O.O.U. (41.16 ± 0.81/bee/colony), respectively. Apiaries in agro-ecosystems within the southwestern region should be properly maintained or managed against infestation of Varroa destructor and Acarapis woodi to prevent an outbreak or spread of the parasites to other apiaries and other areas where beekeeping is being practiced in Nigeria.