Portuniids is the most abundant decapod and also an important resource in crustacean fisheries in Taiwan. However, overfishing has resulted in a decline in the resource. Species identification for fishery resources management, trade and conservation of aquatic species are very important because identify taxa correctly and unambiguously are fundamental. The study was to develop a reliable database that can be used to distinguish different swimming crab species. Mitochondrial DNA 16S rRNA fragments and full sequence of COI gene of 8 crabs from Taiwan were amplified via PCR, and then were purified and sequenced. The phylogenetic tree constructed by using Neighbor-joining method showed that the relationship between genus Portunus and genus Charybdis is more closer than genus Scylla.