Honey bee mites and their population variance in Apis species was studied during autumn, winter, spring, summer and rainy seasons of 2005 at Chitwan. Honey bee mite Tropilaelaps clareae was observed in A. mellifera and A. dorsata colonies where as Varroa destructor (Anderson Trueman) was observed in A. cerana and A. mellifera colonies. The incidence of mites and the level of colony infestation were dependent upon the species of honey bee. Both types of mite infested brood, worker, drone and queen bees. The level of infestation of mites was higher in A. mellifera (78.0%) than in A. cerana (70.0 %) than A. dorsata (50.0 %) bees. Population of T. clareae in colonies of A. mellifera and A. dorsata was the lowest in rainy (6.4 and 3.3 per sample respectively), and the highest in winter and spring season (118.3 and 41.35 per sample respectively). Number of V. destructor was also recorded the lowest in rainy season (4.0 per sample), and the highest in spring (27.7 per sample) season for A. cerana colonies. The population of both kinds of mites began to multiply from autumn and reached at higher damaging level in winter season. Honey bee mite Tropilaelaps clareae, was identified as the major threat to A. mellifera and A. dorsata where vas Varroa destructor was considered threat to A. cerana bees in Nepalese context.