Using 15 species of freshwater prawns (Macrobrachium Bate, 1868) from Taiwan as the study material, characters of mitochondrial 16S rDNA sequences (16S) and nuclear 28S rDNA sequences (28S) were examined. Their phylogenetic analyses were conducted with Bayesian (BI), maximum likelihood (ML), maximum parsimony (MP), and minimum evolution and neighbor-joining (MENJ) methods. The 16S extracted was smaller in sequence length, rich in adenine, poor in cyctosine, and biased strongly to transitions in the nucleotide substitutions, whereas the 28S extracted was larger, rich in guanine, and biased to transversions. In the separate analyses of the two genes, the phylogenetic trees derived from the 28S had appreciably higher topological resolution with deeper branching (less polytomies) and higher topological confidence with stronger phylogenetic signals than the 16S trees. The poor resolution and confidence of the 16S trees were attributable primarily to its poor sequence divergences associated with high transition/transversion (ts/tv) ratios and low α-values of the gamma distributions. The result was a severe convergence of taxa within a narrow range of small genetic distances, so that their bifurcation could not be determined unambiguously. The 28S was highly diverged and had larger genetic distances with low ts/tv ratios and high α-values, resulting in much less convergence of the taxa. The 28S tree reconstructed with BI produced the best topological resolution and confidence in the separate analyses. The partition homogeneity test indicated that the 16S and 28S data sets were congruent. Their combined analyses with ML, MP, and MENJ showed no improvement in both topological resolution and confidence from the separate analyses of the 28S. With BI the combined analysis produced mixed results; improved the estimates of phylogenies for some of the taxa but confused or even obscured for the others.