Interactions between farmers and agrobiodiversity are key drivers of agroecosystems sustainability and of the resilience of such systems to perturbations, but research into the human/nature interactions have overlooked some important aspects of agrobiodiversity management. In particular, farmers' ecological knowledge of the spatial organisation of plant diversity remains an open question, although knowledge and practices have major implications for the efficient and sustainable use of natural resources. • Our study addresses this question by analysing how farmers spatially organise plant species in agroforests based on their knowledge of species interactions and interactions with the environment. The Analanjirofo region on the north-east coast of Madagascar provides an interesting context to explore this issue in clove-based agroforests, as these systems were developed by farmers as a sustainable alternative to the traditional system of shifting rice cultivation. • Using an emic approach, that is based on the farmers' perspective, and participatory mapping, we studied plant diversity and its spatial organisation in 17 clove-based agroforests and in 28 management sub-units defined by farmers in a village of Vavatenina district. The plant functions and farmers' knowledge of plant interactions with clove tree were recorded in semi-structured interviews, and the interactions were represented in a cognitive map. • Farmers manage more than 50 plant species associated with diverse functions. Analysis of participatory maps identified four main types of species association as a function of the age of the clove trees and the associated plant diversity, and different spatial organisation patterns as a function of the topography and the surrounding species. Analysis of farmers' knowledge provided valuable insights into spatial organisation practices, how farmers perceive the adaptation of plant species to biophysical heterogeneity of the environment and whether they can be asso