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Pesticides and inorganic fertilizers applied in agriculture are key factors which affect biodiversity, especially bees, butterfly and other pollinators. Therefore, this study assessed the effects of farming practices on honey production in boundary of Gishwati Forest National Park in Rwanda. Survey was conducted to collect data from 2000 year to 2018 year from 51 members grouped in UNICOAPIGI beekeeping and 73 members of JYAMBERE agricultural cooperatives to establish the impact of agriculture practice on honey production. The results showed that the change in agricultural inputs from 2000 to 2018 (R2 = 0.901) resulted in high corn yield and consequently induced honey reduction (R2 = 0.75). The correlation coefficients for pesticides and inorganic fertilizers used in corn production had strong negative effects on honey production {γ3 = -0.06 for chemical fertilizers (X3) and γ4 = -0.42 for pesticides (X4)}. JYAMBERE Agricultural cooperative with 75.78% of farmers reported that they used pesticides and inorganic fertilizers in corn production. However, 51 beekeepers grouped in UNICOAPIGI cooperative reported a serious decline of honey production from 27 Kg to 6 Kg of honey per hive after the 2008 year, which is suspected to be mainly the effect from applications of pesticides and fertilizers in corn production. The findings illustrated that the roles of honeybees as pollinator exposed them to toxic, especially pesticides applied in agriculture in boundary of Gishwati national forest reserve, therefore, beekeepers proposed that protection of forests and park is not only sufficient to reach sustainable conservation of bee biodiversity but also requires determining the land use pattern and socio-political factors around the Gishwati forest reserve.