Abstract. Ngongo Y, Markus JER. 2020. Agricultural innovations and adaptation strategies among upland communities in the state boundaries of Kupang District (Indonesia) and Oecusse Enclave (East Timor). Trop Drylands 4: 51-57. Development started from the State's periphery has been implemented as a new paradigm or policy of national development in Indonesia. Agricultural Ministry translated this national policy by implementing several programs and one of them is promoting agricultural innovations to boost agricultural production and rural development in the State Boundary. This paper elaborates on agricultural innovations being introduced and adaptations of local people towards harsh climate and to protect natural resources. Data and information used mainly from the on-going program of Agricultural Innovation Support (AIS) in the State Boundary of Kupang District of Republic of Indonesia and Oecusse enclave of Republic Democratic of Timor Leste (East Timor). Some insights of similar programs implemented in the three other districts of Timor that have land borderlines with East Timor have also used to enrich the narratives. Traditional honey beekeeping of Amfoang community used to demonstrate how local people maintain one of the important sources of their livelihoods and at the same time protecting natural resources. The study shows that agricultural innovation being introduced has successfully adopted by co-operators, however, it has limited impacts on the surrounding farmers/villages due to farmers' poor access to the external inputs, market, and agricultural extensions. The paper concludes that agricultural innovations being introduced should be considering farmers’ circumstances, particularly harsh climate of the region, and it should compatible with household calendar both in farming and off-farming particularly in honey harvesting. Recognizing and supporting customary low honey harvesting helps protect forest and biodiversity in Amfoang and Timor in general. Promoting agricultural development and improving infrastructure in the State Boundary should be developed in such a way to strengthen and promotes conservation and protecting biodiversity in fragile ecosystem of Timor.