For clarifying the phylogenetic diversity of fifteen species of the subgenus Ceratotropis, including seven wild and three cultivated Vigna species collected from Myanmar, sequence variations in three trnT-F non-coding regions of the chloroplast genome were analyzed. The Myanmar materials were clustered into two well differentiated groups, the azuki bean group and the mung bean group. Six Myanmar species were clustered into the azuki bean group, and four species into the mung bean group. The azuki bean group consisted of three subclades: angularis-nepalensis subclade, minima subclade and riukiuensis-nakashimae-umbellata-hirtella-exilis subclade. No clear lineage differentiation was found among the three races of V. angularis and V. nepalensis. An accession from Myanmar, which showed similar morphological features to those of wild azuki bean, shared a 51-bp deletion with V. angularis and V. nepalensis. Three V. minima accessions showed a distinct clade. V. riukiuensis showed a nested relationship with V. nakashimae sistered to V. hirtella, V. umbellata and V. exilis. The mung bean group consisted of five radiated subclades. In the mung bean group, V. trinervia from Myanmar was clustered with V. reflexo-pilosa, and wild mung bean accessions with their cultivated accessions. A high level of substitution, indel and microsatellite variations in the trnT-F sequences indicated that mung bean (V. radiata) and black gram (V. mungo) are phylogenetically well differentiated in the mung bean group. Myanmar is considered to be an area overlapping two major groups of the subgenus Ceratotropis.