Uniola paniculata, commonly known as sea oats, is a C4 perennial grass capable of stabilizing sand dunes. The genetic relationship and diversity among U. paniculata accessions from southeastern Atlantic and Gulf coasts of the United States was established by amplified fragment length polymorphism (AFLP) analysis. One hundred ninety U. paniculata plants belonging to nineteen different accessions were selected to represent eight locations; Texas, Louisiana, Mississippi, Alabama, Florida, South Carolina, North Carolina and Virginia. Twelve AFLP EcoRI+MseI primer combinations generated a wide range of polymorphisms (42-81%) with a mean of 59%. EcoRI-CAG+MseI-CGA, EcoRI-ACT+MseI-CTC and EcoRI-CAG+MseI-ACG have the highest polymorphic rate at 81%, 75%, and 72%, respectively. A total of 703 scorable bands were identified of which 417 were polymorphic. UPGMA dendrogram using NTSYSpc version 2.10t separated U. paniculata plants into three major groups with subclusters consistent to its collection sites. All the accessions from Texas (LA2, LA5, LA9 and LA17), Louisiana (LA15 and LA16), and Virginia (LA53) were orderly clustered in Group I together with two accessions from Florida (LA35 and LA39) indicating similar genetic profiles. Group II consisted of accessions from Mississippi (LA41 and LA47), Alabama (LA19 and LA21), and the other two accessions from Florida (LA29 and LA33). Group III comprised South Carolina (NC15 and NC19) and North Carolina (NC1 and NC11) accessions. Dice similarity coefficient shows a range of genetic similarity across all plants from 64-98%. Florida has the widest range of genetic variation among its genotypes followed by Mississippi. The principal component analysis (PCA) further confirmed the three major groups. Hierarchical analysis of molecular variance (AMOVA) after 1000 permutations showed highly significant results (Fst values, p=<0.001) for all the sources of variation. The highest significant amount of genetic variation was observed at the state-level (47%) followed by among-genotypes (34%). Total variation among the accessions within a state was 19%. Calculated average molecular diversity over loci was highest in LA47 (0.07�0.04, Petit Bois Is., Mississippi), LA33 (0.07�0.04, Henderson Beach, Florida), LA15 (0.07�0.04, Fourchon Beach, Louisiana) and LA41 (0.07�0.04, West Ship Is., Mississippi). Overall, the populations of U. paniculata were genetically-diverse.