Species identification for fishery resources management, trading and conserving of aquatic species are very important, as a fundamental first step, requires the ability to identify taxa correctly and unambiguously. DNA barcoding is a diagnostic technique in which short DNA sequences can be used for species identification. The purpose of this project is to establish the database of nucleotide sequences of 16S rRNA and COI gene in mitochondrial DNA for important economic lobster and stomatopoda in Taiwan. Those data can be used as standard sequences in species identification for fishery resources management, trading and conserving of aquatic species; and offered for studies of biology diversity. Family Palinuridae, known as spiny lobsters, are an economically significant food source. Spiny lobsters mainly found in shallow water of 50 m. They tend to live in crevices of rocks and coral reefs. The most common method of catching lobsters is to use gill net and one-way traps located in deep underwater. In current classification systems, the family includes the eight genera Justitia, Palinustus, Linuparus, Puerulus, Panulirus, Palinurus, Jasus and Projasus. DNA barcoding promises a useful tool for species identification, and also to elucidate the phylogeny of spiny lobsters family Palinuridae. We used PCR amplification techniques to successfully establish a molecular identification key for important economic lobster and stomatopoda. Both mitochondrial 16S rRNA and COI fragments of 24 species from Taiwan were amplified via PCR, then the PCR products were purified and sequenced. For COI gene, 653 bp nucleotide sequences were obtained, and which contained 271 divergent sites. Aligned sequences were considerably AT-rich (58.6%). The nucleotide composition showed that A =0.33, C =0.20, G =0.22, and T =0.25. The pairwise genetic distances of lobster species using Kimura 2-parameter model ranged from 0.113 to 0.321.