Cyperus esculentus is an invasive troublesome neophyte in many arable crops across the globe. Analysis of the genetic and morphological profile of local C. esculentus clonal populations may be useful in explaining differential herbicide sensitivity found among distinct clonal populations and spatial distribution patterns. In this study, 35 Belgian C. esculentus clonal populations, evenly spread across the entire infestation area (30,689 km(2)) and covering a great diversity of farm and soil types, and hydrological and environmental conditions, were genetically characterized using amplified fragment length polymorphism (AFLP) profiling. These clonal populations were also grouped into different morphological clusters using data from shoot, tuber, and inflorescence number, fresh tuber biomass, individual fresh tuber weight, and number of germinable seeds collected in three consecutive years. Of the 271 AFLP markers, 207 were polymorphic. The gene diversity among clonal populations was 0.331 and three genetically distinct clusters were identified. Depending on observation year, clonal populations were grouped in four to five morphologically distinct clusters that closely aligned with the genetic clusters. The genetically distinct clusters differed in their geographical distribution pattern and range as well as in their morphological characteristics. Clonal populations belonging to clusters with broad distribution ranges produced numerous viable seeds. Clusters with clonal populations that produced large tubers were less widespread than the cluster with clonal populations producing many small tubers. The results suggest that tuber size, tuber number, and fecundity may all play an important role in the spread of C. esculentus. Morphotyping may be very useful in designing effective preventive and curative C. esculentus management strategies.