Tidal swamp rice has a high genetic diversity and some of the essential genes, so could be useful in developing new rice cultivars in the future. Sixteen cultivars of this germplasm, consisting of fifteen from the South Kalimantan Province and one from Sumatran Island, Indonesia (a comparison) were analyzing, phylogenetically based on the chloroplast trnL-F and nuclear intergenic spacer region (IGS). In general, the chloroplast trnL-F has relatively lower genetic variation than IGS. A combined sequence data set of both sources provided a better resolution of the phylogenetic tree than the individual data sets and showed a unique illustration of monophyletic divergence. The results of our study would provide useful information for further understanding of evolutionary relationships of this germplasm and facilitate the efficient utilization of valuable genes for genetic improvement, particularly in the tidal swamp areas.