Flemingia macrophylla (Willd.) Kuntze ex Merr., a multi-purpose legume with potential as dry-season forage crop, mainly occurs in subhumid to humid environments of tropical and subtropical Asia. Despite increasing interest in conservation of germplasm suitable for low-input production systems information on the genetic diversity of F. macrophylla is extremely scarce. The creation of baseline data is supposed to contribute to more efficient conservation management and to identify collecting strategies of novel germplasm. Random amplified polymorphic (RAPD) markers were used to investigate the genetic variation among 37 F. macrophylla accessions. Germplasm analysed in this study originated from Bac Kan province, Northeast Vietnam. Eight primers generated a total of 47 amplified RAPD loci of which 38 were polymorphic. Jaccard s similarity coefficients among accessions ranged from 0.069 to 1 with a mean of 0.67. The UPGMA dendrogram revealed three clusters along with three outliers. No correspondence between geographic and genetic distance was found (Mantel test: R = 0.21; P = 0.016). Analysis of molecular variance (AMOVA) revealed significant (P < 0.001) differentiation between accessions collected in lowland and upland regions. Results of UPGMA clustering were confirmed by the pattern of principle coordinates analysis (PCO) plotting. Future collecting strategies should target populations at large distances and along the altitudinal range. Ex situ conservation should encompass those accessions that showed genetic divergence. In situ conservation may consist of establishing a system of interconnected population fragments to guarantee continuing genetic exchange via corridors and of rehabilitating degraded habitats.