Enset [Ensete ventricosum (Welw.) Cheesman] is a major multi-purpose crop in Ethiopia, which has been identified as the center of origin and diversity of enset. During the last decades, the local farming systems in which enset is maintained have become endangered. Conservation of clonally propagated crops like enset is complex and relatively expensive. Consequently, an assessment of clonal diversity is essential in order to maximize conservation efforts. In the present study, 146 clones from five different regions in southern and southwestern Ethiopia were characterized with amplified fragment length polymorphisms (AFLPs) to investigate genetic relationships among clones, identify duplicates, and study regional variation. A total of 180 bands were scored, of which 104 (58%) appeared polymorphic. Twenty-one duplication groups consisting of 58 clones were identified. Duplicates were related to different utilization purposes of clones and to the changing of vernacular names after exchange of clones between communities. Despite large variation in agroecological conditions among regions, only 4.8% of the total genetic variation was found between regions, whereas 95.2% was found within regions. This finding may be explained by regular long distance exchange of clones. Furthermore, it suggests the existence of substantial levels of phenotypic plasticity in enset. The results of the study allow for a substantial and well based reduction of the number of clones qualifying for conservation. In addition, the exchange between regions suggested by this study indicates that unexplored additional diversity, if existing, should mainly occur in divergent farming systems.