Population studies and species identification based on morphological characteristics are often ambiguous. A different approach, e.g. molecular information, may be used to clarify the ambiguities . In this thesis, two categories of organisms, fish and corals, were chosen for study. The Danioninae, Candidia barbata and Opsariichthys pachycephalus, are extremely diversified morphologically among the Henchun peninsula and the northern Taiwan populations. Six geographic population of C. barbata were found using the mitochondrial D-loop DNA sequences. The sequences data also confirmed that the Henchun peninsula population was the most divergent group. On the other side of Taiwan strait, Opsariichthys bidens and Zacco platypus in northern Fujian province were also found to be divergent. It is likely that the Danioninae fishes migrated through the basins due to lowering of sea level during glacial stages. The discrepancies of morphological classification and molecular phylogenetics should be re-examined. The five coral mitochondrial genomes sequenced were Euphyllia ancora (19084 bp), Tubastrea aurea (18770 bp), Stylophora pistillata (17169 bp), Montipora aequituberculata (17886 bp), and Junceella fragilis (18724 bp). The gene organization of Octocorallia and Hexacorallia were highly conserved. All the stony corals contain a group I intron in the ND5 gene. In addition, the COI gene of Tubastrea aurea contains an extra intron, which consists an ORF of the LAGLI-DADG gene family. Of all the genes analysed, the transition rates were saturated except COI, COIII, Cytb and ND3; on the other hand, only 12S and ATP8 were saturated for the transversion rates. The results might refer to new gene markers for future species identification of corals.