How enteric nervous system (ENS) circuits are assembled and organized is not well understood. Most ENS neurons and glia are derived from SOX10-expressing enteric neural crest-derived cells (ENCCs). Here, cell-fate mapping showed that ENCCs give rise to clonal clusters of cells in the small intestine, stomach and caecum in mouse embryos, and there was an overlapping spatial distribution of these clonal units in adult mice. Calcium imaging revealed that neurons of the same clonal origin were more likely to show synchronous responses than clonally unrelated neuronal pairs. Thus, ENS organization at spatial and functional levels is cell lineage dependent.