In Malawi, production from subsistence rain fed agriculture is highly vulnerable to climate change and variability. In response to the adverse effects of climate change and variability, a National Adaptation Programme of Action is used as framework for implementing adaptation programmes. However, this framework puts limited significance on indigenous knowledge systems (IKS). In many parts of the world, IKS have shown potential in the development of locally relevant and therefore sustainable adaptation strategies. This study was aimed at assessing the role of IKS in adaptation to climate change and variability in the agricultural sector in a rural district of Chikhwawa, southern Malawi. The study used both qualitative data from focus group and key informant interviews and quantitative data from household interviews and secondary data to address the research objectives. The study established that the local communities are able to recognise the changes in their climate and local environment. Commonly mentioned indicators of changing climatic patterns included delayed and unpredictable onset of rainfall, declining rainfall trends, warming temperatures and increased frequency of prolonged dry spells. An analysis of empirical data corroborates the people’s perception. In addition, the community is able to use their IKS to adapt their agricultural systems to partially offset the effects of climate change. Like vulnerability to climate change, IKS varies over a short spatial scale, providing locally relevant adaptation to impacts of climate change. This paper therefore advocates for the integration of IKS in programmes addressing adaptation to climate change and vulnerability. This will serve to ensure sustainable and relevant adaptation strategies.