Rice cultivation in hills is challenged by sub-optimum weather conditions, low soil fertility, low temperature and moisture stress which impedes in attaining high productivity. To address this, four studies were carried out at ICAR Sikkim Centre, Gangtok, India to evaluate relative performance of local organic cultivars and conventionally bred varieties under an organic farming system. Conventionally bred varieties yielded significantly higher (45%) than local cultivars under recommended timely sown conditions whereas local cultivars showed superiority in grain yield under late sown conditions coinciding with low temperature during flowering to grain filling. Genotypes did not show significant interaction when organic or conventional production conditions were compared. For grain yield, there was a significant variation for variety × year interaction under organic system. Local organic cultivars had reduced grain yield and associated traits under rainfed upland conditions. Panicles per unit area had a significant positive association with grain yield in all production environments (organic lowland, organic upland, conventional lowland and conventional upland). Overall, the study indicates using local cultivars as donors for specific stress tolerance traits in background of high yielding genotypes to enhance rice yields sustainably under organic system in hills.