This paper aims at exploring the impacts of climate change on the marginal communities and the status of silvo-agriculture species. Mahottary district of Nepal was selected for this study in 2012. A pertinent questionnaire was used to determine the impacts of climate change. The key respondents were interviewed and workshops organized at three different levels to triangulate the information. Stratified random sampling was applied to collect the bio-physical data. The results showed a shift in flowering and ripening seasons of agriculture crops. The associate species of Shorea robusta were at threat. Those species were abundant in the past, but rarely found nowadays. The values of Shannon Weinner and Simpson indices were 2.53 and 0.86 respectively in 2005 and 2.34 and 0.85 respectively in January, 2012 showing the impacts of climate change on forest species. Bees that make hive on Bombax ceiba were not found and the marginal communities were affected. Similarly, Terai indigenous communities and Dalits were found to have been affected because of insufficient fish in the paddy fields. Frogs and storks were scarcely found in the farmlands. Extreme drought, untimely floods and mass-wasting have been damaging the wealth and health in the locality.